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revision 1.878 by jmc, Tue Sep 18 21:29:09 2007 UTC revision 1.987 by jmc, Tue May 6 19:02:20 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59q
8    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
9       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
10    o Refresh tutorial_global_oce_biogeo, notably:
11      - change bathymetry (put back seamounts in ACC, use hFacs)
12      - change EOS (POLY3 --> JMD95Z)
13      - use Bryan-Lewis vertical diffusivity
14      - use multidimensional advection
15      - remove old virtual virtual in dic pkg, now done through ptracer pkg
16      - change a couple of parameters in dic pkg
17    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
18    o pkg/obcs: change default to OBCSfixTopo = .true.,
19      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
20      - replace "debugMode" with "debugLevel .GE. debLevB"
21    o implementation of TAF directives for gchem,cfc,dic
22    o remove "exp5" (replaced by tutorial_deep_convection).
23    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
24      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
25      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
26      --> changes results in exp4, seaice_obcs
27    o tutorial_deep_convection :
28      update the set-up and increase resolution and domain size ; start
29      from pseudo initial conditions = output at t=120mn in order to see
30      something happening when running testreport.
31    o pkg/seaice: add os7mp as an advection scheme
32                  add check for advection schemes
33                  add a flag for restoring T and S underneath sea ice
34    o pkg/my82: add netcdf-support and diagnostics
35    o thsice pkg:
36      - Now hsMax limits snow height by turning it into ice following
37        flooding scheme (and now conserving energy)
38      - Slight rewriting of the formula in thsice_calc_thick.F
39      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
40      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
41    
42    checkpoint59p
43    o gchem / dic / cfc :
44      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
45      - add new parameter files: "data.dic" & "data.cfc" ;
46      - various re-arrangement in initialisation & header file ;
47      - fix tutorial_global_oce_biogeo for multi-threaded test.
48    o pkg/dic: test for "pickup_dic" file when restarting ;
49      if no pickup-file, can restart with a re-initialised pH (same as it did
50      before) providing pickupStrictlyMatch is set to False.
51    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
52      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
53    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
54      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
55    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
56     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
57       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
58    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
59       scheme to use for vorticty-term ;
60     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
61       (with default selectVortScheme, return to original discretisation)
62     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
63    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
64    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
65      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
66      also fix diagnostics VISCAHW & VISCA4W.
67    
68    checkpoint59o
69    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
70    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
71      move a few statemens out the main loop into separate loops
72    o pkg/shelfice:
73      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
74        (kg/m^2/s), does not break tests, because in verification/isomip,
75        rhoConstFresh=rhoConst (by accident)
76      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
77      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
78        new file model/src/seawater.F, so that they are available for all pkgs.
79      - convert potential temperature into in-situ temperature. This changes the
80        isomip tests => update tests
81    o add a flag writePickupAtEnd (default=true) to be able to suppress
82      writing a pickup at the last timestep
83    o tools/mpack-1.6 :
84      - disable automake (not working) and autoconf (not needed).
85      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
86        also cleaner with much less compilation warnings.
87    o pkg/profiles:
88      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
89      (for "less than 32 characters name" compiler requirement)
90    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
91      conditions that have a different sampling frequency than S/T/U/V obcs
92    o pkg/diagnostics (stats-diags):
93      - fix global Min/Max in case 1 processor get only empty tiles
94    o genmake2: replace (4 times)
95         make genmake_tc_1.o >> genmake_warnings 2>&1
96      with
97         COMM="$CC $CFLAGS -c genmake_tc_1.c"
98         echo $COMM >> genmake_warnings
99         $COMM >> genmake_warnings 2>&1
100      to make genmake2 always see the value of CC as specified in the optfile.
101    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
102      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
103      - modify verification advect_cs test to test SOM-advection on CS-grid.
104    o pkg/ctrl:
105      - Rewrite of ctrl_map_ini_ecco.F,
106        introducing a generic routine (ctrl_map_ini_gen.F).
107      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
108    
109    checkpoint59n
110    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
111      number in dedicate array "hdiag":
112      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
113        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
114      - many small changes (integer format) for large number of diagnostics
115      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
116        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
117    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
118      usingSphericalGrid, this allows to define the rotated grid coordinates
119      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
120      geographical coordinates according to the inverse of the rotation defined
121      by the Euler angles, so that Coriolis parameter and online-interpolation by
122      exf works with the geographical coordinates on XC/YC/XG/YG.
123      Naturally, this feature does not work with all packages, so some
124      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
125      profiles), because there the coordinates are assumed to be regular
126      spherical grid coordinates.
127    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
128      - introduce isopycnal diffusion coefficient control.
129    o tools/adjoint_options:
130      - additional control vector components.
131    o pkg/mnc: have mnc create marginally meaning full coordinate variables
132      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
133    o pkg/mypackage:
134      - add example of read/write pickup for state-var ;
135      - add entry points to the main code for state-vars diags & write-pickup.
136    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
137      transitions for useExfYearlyFields
138      - add new subroutine that determines the file to read from for
139        use*YearlyFields = .TRUE. and .FALSE.
140      - add a verification experiment to global_with_exf that tests
141        useExfYearlyFields with USE_EXF_INTERPOLATION defined
142    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
143      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
144      subroutines (which could be generated from a template, because they are
145      almost identical), for now they are included in obcs_prescribe_read.F for
146      simplicity
147    o pkg/exf:
148      - add a little more diagnostic to exf_interp_read (in analogy to
149        mds_read_field, can be turned off with debugLevel < debugLevA=1)
150      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
151        ugly but fast by unrolling short inner loops, inserting a unroll=8
152        directive in routine lagran, and splitting a loop and making do while the
153        outermost loop (the latter requires the intoduction of index arrays)
154    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
155    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
156      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
157    o verification/seaice_obcs: updated for restart test and latest options
158    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
159      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
160      for now this is only available for the C-grid code and also within
161      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
162    
163    checkpoint59m
164    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
165      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
166    o gad_som : fix flux output (& diagnostics) to have same units as other  
167      advection scheme fluxes (was previously multiplied by deltaT).  
168    o added verification/seaice_obcs both to test seaice open boundaries
169      and to provide an example matlab scrpt for generating them
170    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
171    o pkg/salt_plume: clean up salt_plume_frac.F to
172      remove redundancy in PlumeMethod 1 and 4
173    o pkg/kpp: added saltplume diagnostics
174    o pkg/obcs and pkg/seaice:
175      - do not set uice and vice to zero when OB*icefile are unspecified
176      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
177      - moved seaice tracer obcs after call to seaice_growth
178    o pkg/salt_plume: added various options for salt plume depth
179      criterion and for vertical distribution of the salt
180    
181    checkpoint59l
182    o pkg/ptracers: new version of ptracers pickup:
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:
186      - add timescale for melting due to warm mixed layer as a means of
187        setting SEAICE_availHeatFrac more conveniently
188      - add a CPP-flag/runtime parameter check for flooding algorithm
189      - reformulated availHeat in seaice_growth.F to be independent of AREA
190    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
191      unit changes
192    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
193    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
194      SX vector computer.
195    o pkg/seaice:
196      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
197        seaice forcing fields can now be read only through pkg/exf
198      - removed some unused halos
199    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
200    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
201      or U/VICE from U/VWIND before computing U/VSTRESS
202    
203    checkpoint59k
204    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
205      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
206    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
207      all experiments pass when compile with un-initialised var. checking option.
208    o added pkg/salt_plume
209    o script to test restart (for now, in MITgcm_contrib/jmc_script)
210    o pkg/seaice: new read/write pickup version.
211      read meta file and write only fields which are needed to restart.
212      ( same logic as main pickup file ; also using pickupStrictlyMatch )
213    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
214    o lab_sea.hb87: modify the domain & update output.hb87.txt :
215      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
216      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
217      process. Fixed here by closing the domain at the Northern boundary.
218    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
219    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
220      a set of consecutive levels in/from a 3-D array.
221    o pkg/ptracers:
222      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
223      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
224    
225    checkpoint59j
226    o in pkgs: dic, obcs, offline, rbcs:
227      standard way to compute coeff. for time interpolation between 2 time reccords
228      which retains full precision (& make results less dependent on compiler).
229      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
230    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
231      packages instead of reading ice cover and wind speed separately
232    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
233     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
234      to allow to compile customized code before the update)
235    o cleaning-up:
236      - fix CPP instruction syntax in pkg/obcs
237      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
238        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
239      - fix some threads issue in IO parts.
240    o pkg/dic:
241      - add tons of "_d 0" (--> much better testreports !)
242       and then update outputs of tutorial_global_oce_biogeo
243    o pkg/mom_fluxform:
244      add a special version of momentum advection intended to conserve momentum
245      next to a bathymetry step or a coastline edge. (default = off = #undef)
246    o new read/write pickup version:
247      - for now, only implemented for main (mdsio) pickup file.
248      - write out only what is needed to restart; merge pickup_nh , pickup_ph
249        and main pickup together.
250      - read meta file; read only what is needed to restart; stop if a field
251        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
252        if it make sense (even if the restart is not perfect).
253      - if no meta file, assume that pickup to read corresponds exactly to
254        a pickup that would currently be written.
255      - read pickup written in the old format (until checkpoint59i) if it
256        recognizes an old meta file (no field-list).
257      - add a meta file in exp. which starts from a pickup: 2 cases:
258        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
259         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
260        b) a meta file describing the content of the associated pickup file
261         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
262    o pkg/mdsio & pkg/rw:
263      - new routine to read a meta file ; new set of routine to read
264        Multiple-fields file (with meta file).
265    o added open boundary conditions capability for seaice
266        HSNOW, HSALT, UICE, and VICE
267    
268    checkpoint59i
269    o adjoint:
270      * fix multiDimAdvection adjoint
271        (partial recomputation problem by TAF for fVerT(:,:,kDown)
272        and comlev1 size definition (maxpass vs. max. number of tracers)
273      * verification/global_ocean.90x45x15 adjoint now tests
274        NLFS and multiDimAdvection using DST3 (=30)
275      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
276    o pkg/kpp: add "_d 0" to real constant (if missing);
277      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
278      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
279    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
280      for internal parameters related to restart process (formerly from PARAMS.h)
281      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
282    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
283      as argument. (only atm2d & obcs write_pickup have not yet been updated)
284    o pkg/monitor:
285      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
286      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
287      - account for deep Atmosphere factor and density factor (anelastic)
288    o added open boundary conditions capability for seaice HEFF and AREA
289    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
290      thermodynamics
291      - requires a little reorganization, which affects the testreport results
292        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
293        so that now the conservative form is tested
294      - add a few comments
295    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
296    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
297    o add new diagnostics to seaice: advective, diffusive fluxes (only for
298      multidim-advection, for scheme 2 they are not filled) and transports,
299      thermodynamic growth rates
300    o change units of EmPmR (inside the code, + within coupling interface)
301      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
302      Affects results @ truncation level (cg2d match) and update output of
303       experiments: lab_sea(6), global_ocean.90x40x15(10),
304      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
305      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
306      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
307      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
308    
309    checkpoint59h
310    o pkg/exf:
311      - improve vectorization by moving if-statement out of loops in
312        exf_mapfields, exf_radiation
313      - exf_bulkformulae.F: introduce 2D fields and vectorize code
314    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
315    o testreport:
316      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
317        monitor & update offline_exf_seaice exp. output.
318      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
319    o pkg/seaice:
320      - bug fix in the evp solver: boundary conditions were affected be
321        masking of zMax/zMin (changes results)
322      - minor bug fix in boundary conditions in seaice_calc_strainrates
323        (changes results for no_slip)
324      - seaice_lsr.F: make interpolation of eta dependent on boundaries
325      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
326      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
327        stress formulation and no-slip boundary conditions
328  o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP  o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
329    in gad_calc_rhs.F ; add few safety stops in initialisation phase.    in gad_calc_rhs.F ; add few safety stops in initialisation phase.
330  o pkg/seaice: a first HSALT time stepping equation has been checked in  o pkg/seaice: a first HSALT time stepping equation has been checked in
# Line 292  o in FFIELDS.h: Line 613  o in FFIELDS.h:
613       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
614  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
615  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
616      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
617        are no longer updating the vertical diffusivity array
618        (passed as argument) but are (re-) setting those arrays.
619  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
620    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
621      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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