/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.942 by dimitri, Fri Jan 18 01:38:33 2008 UTC revision 1.1034 by mlosch, Sat Oct 25 20:49:22 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 fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
8      (#undef REAL4_IS_SLOW)
9     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
10       coordinate variable
11     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
12       (surface forcing fields), removes some of the functionality
13     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
14     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
15       probably not all: copy _RS surface flux fields to RL field before
16       calling DIAGNOSTICS_FILL
17    
18    checkpoint61e
19    o gmredi (Visbeck-variable-K):
20      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
21      - change computation of Visbeck-K where Slope > Smax :        
22        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
23        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
24    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
25      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
26    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
27    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
28      does not become too large (to avoid precision problems in implicit-diffusion
29      solver); update ideal_2D_oce output.
30    o pkg ggl90:
31      - in ggl90_cal.F: compute only one set of visc/diff, used to
32        step forward TKE/T/S/momentum
33      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
34        have Prandlt =1)
35    o gmredi (fm07):
36      - add lower limit on Transition layer thickness + lower limit on 1/lambda
37      - allow to set few more params from data.gmredi
38    o pkg ggl90:
39          - add missing sqrt(2) factor in computation of mixing length
40            scale in ggl90_calc.F
41            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
42    
43    checkpoint61d
44    o adjoint modifs
45      - adapt to new field rhoInSitu
46      - allow to revert from StoreDynVars2D, StoreDynVars3D
47        to individual fields
48        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
49    o store 3-D (in-situ) density in commom block (DYNVARS.h)
50     - save 1 rho computation.
51     - no longer modify T & S inland when using down_slope pkg.
52    o gad_som : allow to switch to SOM advection for T & S without corresponding
53      pickup files (using new S/R: MDS_CHECK4FILE).
54    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
55      (for useSingleCpuIO to work in multi-threaded)
56    o pkg/shelfice:
57     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
58       with SHELFICEtopoFile in data.shelfice
59     - move code for reading ice shelf topography and modifying hFacC into separate
60       subroutines of the shelfice package
61     - separate initialisation of "fixed" and "variable" variables
62     - kTopC is not (yet) replaced by kSurfC, although this is possible
63    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
64    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
65      and rename:
66      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
67      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
68    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
69    
70    checkpoint61c
71    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
72      to add mass source/sink of fluid in the interior (3-D generalisation
73      of oceanic real-fresh water flux).
74    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
75    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
76    o new pkg: down_slope
77      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
78      - presently, modify T & S inland (dwnslp_calc_rho.F).
79        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
80      - implementation for ocean in P-coords not tested.
81      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
82    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
83      (to facilitate conversion of oceanic pkg to p-coordinate).
84    o change FIND_RHO to FIND_RHO_2D :
85      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
86    o new pkg: cheapaml
87    
88    checkpoint61b
89    o exch2:
90      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
91      - no longer depend on the order sequence (N,S,E,W).
92      - 3rd exchange no longer needed (tested with 24 tiles).
93      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
94      - exch_UV_A-grid readily available (but not yet tested).
95      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
96      (both are no longer needed) in exch_uv: no effect in forward run; but
97       get truncation error differences with adjoint exch.
98    o exch2:
99     - change index-bounds storage (moved from target to local tile,
100       more intuitive this way) ; rename/remove some variables.
101     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
102    
103    checkpoint61a
104    o exch2/matlab-topology-generator:
105      fix bug in index bounds for N-S internal exchange (hard to tell if this
106      had any effect on the solution).
107    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
108      is exceeded
109    o testreport: modify syntax of awk, so that it works also with
110      awk, and not only with nawk and gawk
111    
112    checkpoint61
113    o autodiff
114      Change default for TAF usage by removing argument '-nonew_arg'
115      This changes TAF subroutine argument list (ordering of active var.)
116      Omission of this flag leads to incompatibility w.r.t. TAMC
117      To restore TAMC-compatibility, need following modifs:
118      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
119      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
120      Tested TAF version is 1.9.22
121      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
122    
123    checkpoint60
124    --->>> This is the last checkpoint for which generating the adjoint
125    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
126    --->>> by default.
127    --->>> Future checkpoints will ommit this flag by default.
128    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
129    o pkg/grdchk: Add gradient check to etan0 perturbations.
130    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
131    o pkg/autodiff: more flexibility in zeroadj.
132      model/src: modifying do_oceanic_phys.F accordingly.
133    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
134    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
135      special setup of gmredi for which the adjoint is stable
136      enough for parameter optimization.
137    o bridging the gap between eddy stress and GM.
138      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
139          along with a change in CPP option (now ALLOW_EDDYPSI).
140      -> when using GM w/ GM_AdvForm:
141          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
142          is applied either in the tracer Eq. or in momentum Eq.
143          depending on data.gmredi (intro. GM_InMomAsStress).
144      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
145      The key modifications are in model/src/taueddy_external_forcing.F
146      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
147    
148    checkpoint59r
149    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
150      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
151      fix option to read coriolis(@ cell-corner) from files with CS-grid.
152    o pkg/mnc: add some attributes to standard 1D-coordinate variables
153    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
154      mass points, when using mnc for output
155      - add runtime parameter (missing_value, missing_value_int) to override
156        default (which is the value of getcon('UNDEF'))
157    o pkg/mnc: prepare mnc for the actual use of missing values with the
158      diagnostics package: small fix in mnc_cw_readwrite.template and more
159      initialisation of never used fields
160      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
161      versions
162    o pkg/thsice/thsice_ini_vars.F added default initial values so that
163      thermodynamics sea ice solver does not blow up when some initial fields
164      are missing.
165    o move from external_forcing_surf.F to ini_forcing.F
166      the p-coord. hack consisting in using pLoad to set phi0surf ;
167      update output of tutorial_global_oce_in_p (affected @ truncation level).
168    o Freshen up a bit hs94.1x64x5, notably:
169      remove rotationPeriod and tRef=5*0. (adjoint only), and add
170      exactConserv=.TRUE.
171    o pkg/generic_advdiff:
172      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
173      applies to files where Temperature & Salinity 2nd Order moments are used.
174    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
175      this uses a dynamically allocated internal state data structure
176      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
177      and requires a fortran 90 compiler
178    
179    checkpoint59q
180    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
181       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
182    o Refresh tutorial_global_oce_biogeo, notably:
183      - change bathymetry (put back seamounts in ACC, use hFacs)
184      - change EOS (POLY3 --> JMD95Z)
185      - use Bryan-Lewis vertical diffusivity
186      - use multidimensional advection
187      - remove old virtual virtual in dic pkg, now done through ptracer pkg
188      - change a couple of parameters in dic pkg
189    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
190    o pkg/obcs: change default to OBCSfixTopo = .true.,
191      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
192      - replace "debugMode" with "debugLevel .GE. debLevB"
193    o implementation of TAF directives for gchem,cfc,dic
194    o remove "exp5" (replaced by tutorial_deep_convection).
195    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
196      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
197      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
198      --> changes results in exp4, seaice_obcs
199    o tutorial_deep_convection :
200      update the set-up and increase resolution and domain size ; start
201      from pseudo initial conditions = output at t=120mn in order to see
202      something happening when running testreport.
203    o pkg/seaice: add os7mp as an advection scheme
204                  add check for advection schemes
205                  add a flag for restoring T and S underneath sea ice
206    o pkg/my82: add netcdf-support and diagnostics
207    o thsice pkg:
208      - Now hsMax limits snow height by turning it into ice following
209        flooding scheme (and now conserving energy)
210      - Slight rewriting of the formula in thsice_calc_thick.F
211      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
212      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
213    
214    checkpoint59p
215    o gchem / dic / cfc :
216      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
217      - add new parameter files: "data.dic" & "data.cfc" ;
218      - various re-arrangement in initialisation & header file ;
219      - fix tutorial_global_oce_biogeo for multi-threaded test.
220    o pkg/dic: test for "pickup_dic" file when restarting ;
221      if no pickup-file, can restart with a re-initialised pH (same as it did
222      before) providing pickupStrictlyMatch is set to False.
223    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
224      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
225    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
226      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
227    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
228     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
229       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
230    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
231       scheme to use for vorticty-term ;
232     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
233       (with default selectVortScheme, return to original discretisation)
234     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
235    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
236    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
237      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
238      also fix diagnostics VISCAHW & VISCA4W.
239    
240    checkpoint59o
241    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
242    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
243      move a few statemens out the main loop into separate loops
244    o pkg/shelfice:
245      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
246        (kg/m^2/s), does not break tests, because in verification/isomip,
247        rhoConstFresh=rhoConst (by accident)
248      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
249      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
250        new file model/src/seawater.F, so that they are available for all pkgs.
251      - convert potential temperature into in-situ temperature. This changes the
252        isomip tests => update tests
253    o add a flag writePickupAtEnd (default=true) to be able to suppress
254      writing a pickup at the last timestep
255    o tools/mpack-1.6 :
256      - disable automake (not working) and autoconf (not needed).
257      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
258        also cleaner with much less compilation warnings.
259    o pkg/profiles:
260      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
261      (for "less than 32 characters name" compiler requirement)
262    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
263      conditions that have a different sampling frequency than S/T/U/V obcs
264    o pkg/diagnostics (stats-diags):
265      - fix global Min/Max in case 1 processor get only empty tiles
266    o genmake2: replace (4 times)
267         make genmake_tc_1.o >> genmake_warnings 2>&1
268      with
269         COMM="$CC $CFLAGS -c genmake_tc_1.c"
270         echo $COMM >> genmake_warnings
271         $COMM >> genmake_warnings 2>&1
272      to make genmake2 always see the value of CC as specified in the optfile.
273    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
274      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
275      - modify verification advect_cs test to test SOM-advection on CS-grid.
276    o pkg/ctrl:
277      - Rewrite of ctrl_map_ini_ecco.F,
278        introducing a generic routine (ctrl_map_ini_gen.F).
279      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
280    
281    checkpoint59n
282    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
283      number in dedicate array "hdiag":
284      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
285        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
286      - many small changes (integer format) for large number of diagnostics
287      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
288        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
289    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
290      usingSphericalGrid, this allows to define the rotated grid coordinates
291      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
292      geographical coordinates according to the inverse of the rotation defined
293      by the Euler angles, so that Coriolis parameter and online-interpolation by
294      exf works with the geographical coordinates on XC/YC/XG/YG.
295      Naturally, this feature does not work with all packages, so some
296      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
297      profiles), because there the coordinates are assumed to be regular
298      spherical grid coordinates.
299    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
300      - introduce isopycnal diffusion coefficient control.
301    o tools/adjoint_options:
302      - additional control vector components.
303    o pkg/mnc: have mnc create marginally meaning full coordinate variables
304      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
305    o pkg/mypackage:
306      - add example of read/write pickup for state-var ;
307      - add entry points to the main code for state-vars diags & write-pickup.
308    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
309      transitions for useExfYearlyFields
310      - add new subroutine that determines the file to read from for
311        use*YearlyFields = .TRUE. and .FALSE.
312      - add a verification experiment to global_with_exf that tests
313        useExfYearlyFields with USE_EXF_INTERPOLATION defined
314    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
315      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
316      subroutines (which could be generated from a template, because they are
317      almost identical), for now they are included in obcs_prescribe_read.F for
318      simplicity
319    o pkg/exf:
320      - add a little more diagnostic to exf_interp_read (in analogy to
321        mds_read_field, can be turned off with debugLevel < debugLevA=1)
322      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
323        ugly but fast by unrolling short inner loops, inserting a unroll=8
324        directive in routine lagran, and splitting a loop and making do while the
325        outermost loop (the latter requires the intoduction of index arrays)
326  o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice  o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
327  o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver  o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
328    http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html    http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html

Legend:
Removed from v.1.942  
changed lines
  Added in v.1.1034

  ViewVC Help
Powered by ViewVC 1.1.22