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revision 1.1457 by heimbach, Fri Jun 17 13:33:55 2011 UTC revision 1.1502 by jmc, Wed Sep 21 16:29:49 2011 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/exch2:
8      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
9        many tiles); until alternative coding is added, just add a stop.
10    o pkg/kpp:
11      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
12        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
13    o optfiles:
14      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
15        into corresponding standard one, which now support different build:
16        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
17      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
18    o pkg/obcs (seaice):
19      - add missing EXCH for uIce,vIce after applying OBCS;
20      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
21        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
22        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
23      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
24      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
25        and eedata.mth for MPI and mutlti-threaded testing.
26    o pkg/flt:
27      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
28      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
29      - fix pickup and trajectories + profiles output with multi-threads;
30      - add parameter to select group of fields to write along trajectory and
31        profile (default unchanged);
32      - only call PORT_RAND* function when flt_noise <> 0;
33      - add multi-threaded test for verification exp. flt_example.
34    o eesupp/src:
35      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
36      - USE_OMP_THREADING: check that number of threads (from eedata) matches
37        actual number (from env.var. setting).
38    o pkg/ebm:
39      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
40      - add multi-threaded test for verification exp. global_ocean_ebm
41    
42    checkpoint63b (2011/08/29)
43    o pkg/ebm:
44      - fix sign of runoff;
45      - update directly forcing fields (Qnet,EmPmR) to use standard
46        external_forcing_surf.F (remove ebm_forcing_surf.F);
47      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
48      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
49        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
50      - update global_ocean_ebm parameters file data and update output (fwd+ad).
51    o verification/matrix_example:
52      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
53        MPI and mutlti-threaded testing.
54    o pkg/matrix:
55      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
56      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
57      - fix for multi-threaded (remove DATA statement);
58      - use standard DIFFERENT_MULTIPLE function;
59      - add MATRIX_OPTIONS.h
60    o verification/matrix_example:
61       To allow to split the domain in several tiles, change the domain size
62        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
63        Western side) of land points.
64    o (*_)write_pickup:
65      - fix few bugs in mypackage_read/write_pickup.F
66      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
67        array of length 1 (was caught by compiler syntax-check).
68    o pkg/diagnostics (velocity potential solver):
69      - fix initialisation of main diagonal matrix (for overlap values)
70    o tools/build_options:
71      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
72        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
73      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
74        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
75        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
76        and use "-devel" testreport option for standard testing on baudelaire.
77    o pkg/grdchk:
78      - Assume that all gradient-check position are within the same tile
79        corresponding to global indices (iGloTile,jGloTile) and that
80        positions (i,j indices or nbeg) are local to this tile;
81      - set tile local-indices and proc. number according to tile global-indices;
82      - remove grdchkwhichproc from namelist (retired param);
83      - send adjoint gradient to all procs so that all procs print it to STDOUT;
84      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
85    o adding package bbl (Bottom Boundary Layer)
86      description in MITgcm/pkg/bbl/bbl_description.tex
87      example/test experiment in MITgcm_contrib/bbl
88    o adjoint verifications
89      - changed 5 experiments to multi-tiles
90        * global_ocean.90x40x15
91        * obcs_ctrl
92        * offline_exf_seaice
93        * tutorial_dic_adjoffline
94        * tutorial_tracer_adjsens
95        changed reference output for those that crossed tile boundaries
96        (changed choices of gradient check positions)
97      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
98      - temporary bug fix in grdchk_loc.F for obcs
99    o genmake2 & testreport
100      - add target "obj" (just for OBJFILES files) to Makefile;
101      - add option to specify FEXTRAFLAGS on command line.
102    o pkg/mypackage:
103      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
104    
105    checkpoint63a (2011/08/02)
106    o pkg/diagnostics (velocity potential):
107      - fix velocity-potential calculation when using OBCS: balance net inflow
108        at each level (new S/R OBCS_DIAG_BALANCE).
109      - fix some of the problems with OBCS in stream-function calculation.
110    o pkg/exf/exf_readparms.F
111      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
112        EXF_NML_OBCS) more consistent, so that you need not have these lists
113        in data.exf when they are not used.
114    o optim/optim_readdata.F:
115      - add some output about obcs variables that might help debugging
116      - add a check about nvarlength
117    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
118    o pkg/diagnostics (velocity potential):
119      - fix mask for OBCS (still problems in stream-function with OBCS);
120      - add specific parameter (default = main code CG2D params) for solver;
121      - in case of poor convergence, use solution corresponding to lowest residual.
122    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
123      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
124      and should be avoided where possible.
125    o model/src (rStar):
126      - include r* effect on reference-state (PhiRef) in totPhiHyd
127        (so that it's really the potential anomaly at the cell center);
128        affect solution only if z* with full pressure in EOS.
129      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
130        update output (because of z* in totPhiHyd and viscA4 changes);
131      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
132        @ constant r) until interpolation at constant r is implemented.
133    o pkg/diagnostics
134      - fix RCENTER diagnostics in case cell center is not at interface middle
135    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
136      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
137      that THETA and SALT are "conservative temperature" and "absolute
138      salinity"
139    o pkg/ctrl
140      - fix computation of endrec in s/r ctrl_init_rec
141      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
142    o pkg/seaice/seaice_growth.F
143      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
144        remove then obsolete STORE directives
145      - fix STORE directives for tice and tices, so that only the
146        appropriate part of the fields are stored (and not the entire
147        field); update global_ocean.cs32x15.seaice AD output.
148      - cosmetic changes: adjust CPP flags and indentation for better
149        legibilty
150    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
151      Chris Wilson)
152    o pkg/gmredi:
153       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
154       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
155    
156    checkpoint63  (2011/07/11)
157    o pkg/exch2:
158     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
159     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
160       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
161       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
162    o pkg/diagnostics:
163     - deal with pairs of post-processed diags which are computed together; in
164       particular, re-order list of diags within 1 file to save 2nd computation.
165     - add S/R to compute velocity stream-function (called after velocity-potential
166       calculation) from divergence free transport -> new diagnostics "PsiVEL".
167     - add parameter to select grid-point location where PsiVEL == 0.
168    o eesupp/src:
169       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
170       (specific S/R needed with exch2 topology - for now, just print an error msg)
171    o pkg/shelfice
172     - Implement friction velocity-dependent transfer coefficients following
173       Holland and Jenkins, JPO, 1999
174       Original code by M. Losch with small modifs.
175       Enable with CPP option SHI_ALLOW_GAMMAFRICT
176       and runtime flag SHELFICEuseGammaFrict
177    o verification lab_sea & global_ocean.cs32x15:
178     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
179       does not miss some dependencies (but is slower) and also works with many files
180       (default makedepend limitation for AD built).
181     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
182    o pkg/diagnostics:
183     - add run-time parameter "useMissingValue" (def=False) to fill land-point
184        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
185       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
186     - Extend the use of "missing_value" setting from data.diagnostics for the case
187       of counter-diagnostics (where fraction-weight is zero). This applies both to
188       MNC and MDS output files.
189    o pkg/seaice/seaice_growth.F:
190      - add 'a priori' cap of latent heat flux based on actual mass considerations
191        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
192        non-legacy seaice_solve4temp.
193      - add diagnostic of the residual sublimation freshwater flux (the freshwater
194        flux taken from the ocean if the total actual latent heat fluxes exceed
195        the maximum)
196      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
197       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
198      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
199       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
200      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
201      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
202    o verification 1D_ocean_ice_column:
203       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
204       update results
205    o pkg/diagnostics:
206     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
207       which are not filled-up but computed from other diags ; In this case, the mate
208       diag points to the primary (filled-up) diag to used for post processing.
209     - Update Velocity-potential computation using post-processed diag framework.
210     ==> Change the ordering of fields and time-periods in MDS output file
211       when using periodic averaging: now writes one time record with the full set
212       of fields for this time period, then the next time reccord (it used to be
213       one field with the full set of time records then the next field).
214         Note: this is now similar to NetCDF (MNC) output file. <==
215    
216    checkpoint62z (2011/06/21)
217  o adjoint monitor:  o adjoint monitor:
218   - Add adjoint monitor output for packages exf, seaice   - Add adjoint monitor output for packages exf, seaice
219     and update relevant testreport output     and update relevant testreport output
# Line 14  o pkg/seaice: Line 224  o pkg/seaice:
224   - modified diag: SIdA; output actual effect, as the description states.   - modified diag: SIdA; output actual effect, as the description states.
225   - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.   - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
226   - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.   - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
227     (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;     (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
228      and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)      and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
229   - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.   - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
230   - added diagnostics for seaice genereic tracers (SItr*).   - added diagnostics for seaice generic tracers (SItr*).
231   - added SItrUnit and SItrNameLong run time param (for SItr* diags).   - added SItrUnit and SItrNameLong run time param (for SItr* diags).
232   - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.   - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
233     I. Fenty: 18-Jun-2011:
234     Minor changes to seaice package:
235     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
236        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
237       - Differentiated "regularization variables" from "floor variables"
238        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
239        * hiceMin became SEAICE_hice_reg (old hiceMin)
240          (with _reg meaning regularization variable)
241       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
242        so as to ensure energy conservation when going between phases
243      - A22 was not used anywhere
244     2) Changed regularization procedure for heffActual and hsnowActual to ensure
245        well-boundedness and smooth adjoint in seaice_growth.F
246     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
247        because the old regularization always set heffActual >= 0.05 cm
248     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
249        on AREA when HEFF > 0.
250      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
251        requiring that DISABLE_AREA_FLOOR *not* be defined
252     Affected verifications:
253      - 1D_ocean_ice_column (output.txt output_adm.txt)
254      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
255  o pkg/diagnostics:  o pkg/diagnostics:
256    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
257    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
# Line 27  o pkg/diagnostics: Line 259  o pkg/diagnostics:
259    - add pieces of code to compute velocity potential at each level (new diagnostics    - add pieces of code to compute velocity potential at each level (new diagnostics
260      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
261      for now, using same params as CG2D (target-resisual, max Nb of iter ...).      for now, using same params as CG2D (target-resisual, max Nb of iter ...).
262      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
263        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
264        and in diagnostics_fract_fill.F (do not need a valid pointer for the
265        diagnostics counter-mate); check that definition of counter-diagnostic
266        includes a valid counter-mate (in diagnostics_set_levels.F).
267  o model/src (rStar):  o model/src (rStar):
268    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
269      affect solution only if z* with full pressure in EOS;      affect solution only if z* with full pressure in EOS;
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