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revision 1.808 by jmc, Thu May 3 22:57:27 2007 UTC revision 1.1108 by dfer, Wed May 27 03:12:04 2009 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 computations of L4rdt in mom_calc_visc.F
8    o eesupp:
9      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
10      should be called before a "stop" if we know that all process are going
11      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
12    
13    checkpoint61o
14    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
15    o model/src/ini_curvilinear_grid.F:
16       compute angleSin/CosC when they are not read from a file
17    o pkg/seaice:
18       add pseudo time stepping for LSOR
19    o pkg/exch2:
20       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
21    o pkg/seaice:
22       Adding separate sea ice albedo, drag coefficients, and HO in Southern
23       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
24    o SingleCpuIO:
25       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
26    o pkg/seaice:
27       put exchanged variable in (local) common block for MPI+Multi-Threads
28       to work (necessary with exch1, and for now with exch2 too).
29    o verification: to get more experiments tested with mpi, mth and mpi+mth,
30      change tiling of:
31       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
32       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
33      update output of exp:
34       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
35       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
36      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
37                       (note: output.txt generated on faulks using only 1 tile)
38    o eesupp & mdsio (SingleCpuIO):
39     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
40       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
41       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
42     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
43     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
44       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
45    o pkg/exch2:
46     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
47       read parameter file "data.exch2" if it exists; otherwise try default regular
48       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
49     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
50       with new code (not to be used, just as a backup solution).
51     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
52       in utils/exch2/input.
53    
54    checkpoint61n
55    o eesupp & mdsio (SingleCpuIO):
56      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
57        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
58        receive real*4 array (instead of real*8) to read/write 32.bit files.
59        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
60         and remove new mapping S/R)
61    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
62      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
63        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
64        when using exch2. Add S/R to map global io-buffer to global model array.
65      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
66    
67    checkpoint61m
68    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
69      and add 3 other S/R for other types (R4,R8,RS).
70      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
71    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
72     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
73     - reduce number of macro definitions (keep only those which are used);
74       can always call directly the corrresponding S/R if needed.
75     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
76       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
77     Fixed wrong type of arg in:
78       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
79       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
80     To fix: global_sum of var in common block is wrong (multi-threaded) in:
81       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
82     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
83    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
84      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
85    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
86    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
87      edges are closed (zero depth); might happen with "blank tiles";
88      for now, disabled if using OBCS.
89    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
90      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
91    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
92      to reduce length of 1.D array print in STDOUT.
93    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
94      + use 48 tiles (16x8): this will allow to test "blank tiles".
95    o start to test MPI + multi-threaded (change testreport to skip tests
96      where number of tiles do not match).
97    o genmake2: add option "-omp" to turn on Open-MP ;
98      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
99    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
100      and keep the original tile numbering. Note: compatible with old
101      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
102    
103    checkpoint61l
104    o Overlaps had been forgotten in calculating ijk keys : fixed
105    o fix cyrus makedepend for gcc 4.4
106    o experiment fizhi-cs-aqualev20:
107      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
108      and generate new output. Note: new output is much closer to the old
109      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
110      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
111    o pkg/fizhi:
112     - change to avoid indices going deliberately over array-bounds
113     - remove unnecessary MPI stuff
114     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
115     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
116       does not go over array-bounds and therefore returns reliable output.
117     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
118       this S/R has 4 output arguments, which are used inside "get_alarm";
119       when it is called with the same variable "ndum" in place of several
120       output arguments, this produces weird side effect inside "get_alarm"
121      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
122       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
123       address) and produces error.
124    o tools/gemake2: (March 27-29 2009)
125      with option "-mpi": link *_mpi files from "MODS" dir (this is what
126      testreport does).
127    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
128    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
129       update lab_sea.lsr & lab_sea.salt_plume results
130    o pkg/seaice:
131      Major overhaul of the LSOR solver: change discretization from original
132      finite differences to finite volume. The old routine is still in the
133      file seaice_lsr.F and can be turned on with the CPP-flag
134      SEAICE_OLD_AND_BAD_DISCRETIZATION
135      Along with this change, the discretization of the strain rates is changed.
136      The same flag turns on the old discretization in seaice_calc_strainrates.F
137      All verification experiments with seaice are affected (except for
138      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
139      results by setting the above flag.
140      Further changes involve changes in defaults:
141      - ALLOW_FLOODING is defined and turned on by default
142      - SEAICEadvSnow = .true. is now the default
143      - SEAICEadvSalt = .true. is now the default
144      - SEAICEadvAge  = .true. is now the default
145      - SEAICE_clipVelocities  = .false. is now the default
146                                         (as per J. Zhang's recommendation)
147      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
148        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
149      - seaice_growth: replace computation of UG by a simple copy from wspeed
150    
151    checkpoint61k
152    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
153      seaice_lsr: fixed a few metric terms,
154                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
155                  add more debugging diagnostics
156      seaice_evp: removed superfluous many metric terms of FV discretization
157                  of stress divergence
158                  affects lab_sea, lab_sea.hb87
159      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
160                  of stress divergence for non-evp solver
161                  (this part is not tested anywhere)
162      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
163                  they were effectively only half slip
164                  affects lab_sea.hb87
165      updated all relevant verification experiments (except lab_sea//output_adm.txt
166        which was left over, but fails at level 7 & 6)
167    
168    checkpoint61j
169    o pkg/seaice: turn a few hard wired parameters into run time parameters
170    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
171      time in seconds as promised by the usints in seaice_monitor and exf_monitor
172    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
173      that are not cubed-sphere grids
174    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
175    o pkg/ctrl:
176      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
177    o non-hydrostatic (calc_gw.F):
178      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
179      update output of exp. global_ocean.cs32x15.viscA4
180    o remove backward compatibility for thetaMin,phiMin
181      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
182    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
183      interpolated wind field not only for curvilineargrid=.true., but also
184      for a rotated grid (rotateGrid=.true.)
185    o pkg/exf: add capability to bypass interpolation for runoff
186      by setting yet another CPP-flag
187    o eesupp/src, B-grid exchange:
188      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
189    o autodiff
190      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
191      allows to switch to single-prec common blocks;
192      corresponding switch occurs in tamc.h, integer isbyte
193      TAF store directivs "byte" and "kind" seem equivalent;
194      Most tamc.h have been updated correspondingly.
195    
196    checkpoint61i
197    o autodiff:
198      fix autodiff_sore/_restore indices for obcs
199      (spotted by I. Hoteit, M. Mazloff)
200    o pkg/autodiff, pkg/ctrl:
201      Add flag to reduce all tapelev I/O to single-prec.
202      In data.ctrl set
203        doSinglePrecTapelev = .TRUE.
204    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
205      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
206    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
207      real fresh water flux (not yet)
208    o pkg/mdsio & rw:
209     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
210     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
211    o pkg/flt:
212     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
213       init_fixed & ini_varia.
214     - clean-up & simplify linear interpolation S/R:
215       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
216     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
217     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
218     - add vert. coordinate & horiz. indices to output files.
219     - change vertical position in initial condition, from index to depth [m].
220     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
221       (easier to get to a curvilinear grid) ; delX,delY no longer used.
222    o pkg/ggl90: a few modifications:
223     - fix bottom boundary condition, and interpolation of KappaE
224       near top and bottom
225     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
226     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
227     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
228    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
229      (maintain temporary backward compatibility, until next checkpoint)
230    
231    checkpoint61h
232    o pkg/diagnostics with "periodic averaging diagnostics":
233      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
234    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
235    o pkg/obcs: fix loop ranges for balancing code
236    o pkg/flt:
237     - improve criteria for finding which tile owns a float.
238     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
239    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
240      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
241      with ocean biogeo)
242    o pkg/flt:
243     - do some cleaning and fix the restart ;
244     - add output.txt in flt_example/results to get this pkg tested.
245    o genmake2: add an EXTENDED_SRC option and flag.
246       for now, cannot be turned on on command line (only through genmake_local)
247    o pkg/mdsio: read/write vector:
248     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
249     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
250       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
251     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
252      (drop to 4 digits matching for grad). But this test does not look very
253      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
254    
255    checkpoint61g
256    o pkg/flt:
257      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
258       + make OPTIONS file more standard.
259      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
260      - fix _BYTESWAPIO CPP-Flag
261      - standard reading of file-parameter "data.flt"
262      - fix argument list of S/R FLT_RESTART
263      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
264    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
265    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
266      a still unfixed compiler/optimization bug
267    
268    checkpoint61f
269    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
270      update results of global_ocean.cs32x15.icedyn test.
271    o move getcon.F from model/src to pkg/fizhi.
272    o pkg/exf: add parameter for extrapolation of temp up to the surface
273       and option to prevent negative evap (in bulk_largeyeager04 only).
274    o Prather Advection scheme: fix tracer conservation for divergent flow
275      (e.g., when using NonLin Free-Surface).
276    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
277    o gmredi (Visbeck-variable-K):
278     - add more parameters to Visbeck-variable-K.
279     - use a 5 points average for dSigmaR in Visbeck-K calculation
280       (more "homogenous": same stencil and same weights as in dSigmaH)
281     - update output of ideal_2D_oce experiment.
282    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
283      (#undef REAL4_IS_SLOW)
284     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
285       coordinate variable
286     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
287       (surface forcing fields), removes some of the functionality
288     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
289     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
290       probably not all: copy _RS surface flux fields to RL field before
291       calling DIAGNOSTICS_FILL
292     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
293       real*4 (CALL EXCH_*_RS) versions.
294     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
295       (generate new output).
296    
297    checkpoint61e
298    o gmredi (Visbeck-variable-K):
299      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
300      - change computation of Visbeck-K where Slope > Smax :        
301        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
302        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
303    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
304      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
305    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
306    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
307      does not become too large (to avoid precision problems in implicit-diffusion
308      solver); update ideal_2D_oce output.
309    o pkg ggl90:
310      - in ggl90_cal.F: compute only one set of visc/diff, used to
311        step forward TKE/T/S/momentum
312      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
313        have Prandlt =1)
314    o gmredi (fm07):
315      - add lower limit on Transition layer thickness + lower limit on 1/lambda
316      - allow to set few more params from data.gmredi
317    o pkg ggl90:
318          - add missing sqrt(2) factor in computation of mixing length
319            scale in ggl90_calc.F
320            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
321    
322    checkpoint61d
323    o adjoint modifs
324      - adapt to new field rhoInSitu
325      - allow to revert from StoreDynVars2D, StoreDynVars3D
326        to individual fields
327        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
328    o store 3-D (in-situ) density in commom block (DYNVARS.h)
329     - save 1 rho computation.
330     - no longer modify T & S inland when using down_slope pkg.
331    o gad_som : allow to switch to SOM advection for T & S without corresponding
332      pickup files (using new S/R: MDS_CHECK4FILE).
333    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
334      (for useSingleCpuIO to work in multi-threaded)
335    o pkg/shelfice:
336     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
337       with SHELFICEtopoFile in data.shelfice
338     - move code for reading ice shelf topography and modifying hFacC into separate
339       subroutines of the shelfice package
340     - separate initialisation of "fixed" and "variable" variables
341     - kTopC is not (yet) replaced by kSurfC, although this is possible
342    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
343    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
344      and rename:
345      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
346      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
347    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
348    
349    checkpoint61c
350    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
351      to add mass source/sink of fluid in the interior (3-D generalisation
352      of oceanic real-fresh water flux).
353    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
354    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
355    o new pkg: down_slope
356      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
357      - presently, modify T & S inland (dwnslp_calc_rho.F).
358        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
359      - implementation for ocean in P-coords not tested.
360      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
361    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
362      (to facilitate conversion of oceanic pkg to p-coordinate).
363    o change FIND_RHO to FIND_RHO_2D :
364      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
365    o new pkg: cheapaml
366    
367    checkpoint61b
368    o exch2:
369      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
370      - no longer depend on the order sequence (N,S,E,W).
371      - 3rd exchange no longer needed (tested with 24 tiles).
372      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
373      - exch_UV_A-grid readily available (but not yet tested).
374      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
375      (both are no longer needed) in exch_uv: no effect in forward run; but
376       get truncation error differences with adjoint exch.
377    o exch2:
378     - change index-bounds storage (moved from target to local tile,
379       more intuitive this way) ; rename/remove some variables.
380     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
381    
382    checkpoint61a
383    o exch2/matlab-topology-generator:
384      fix bug in index bounds for N-S internal exchange (hard to tell if this
385      had any effect on the solution).
386    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
387      is exceeded
388    o testreport: modify syntax of awk, so that it works also with
389      awk, and not only with nawk and gawk
390    
391    checkpoint61
392    o autodiff
393      Change default for TAF usage by removing argument '-nonew_arg'
394      This changes TAF subroutine argument list (ordering of active var.)
395      Omission of this flag leads to incompatibility w.r.t. TAMC
396      To restore TAMC-compatibility, need following modifs:
397      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
398      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
399      Tested TAF version is 1.9.22
400      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
401    
402    checkpoint60
403    --->>> This is the last checkpoint for which generating the adjoint
404    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
405    --->>> by default.
406    --->>> Future checkpoints will ommit this flag by default.
407    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
408    o pkg/grdchk: Add gradient check to etan0 perturbations.
409    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
410    o pkg/autodiff: more flexibility in zeroadj.
411      model/src: modifying do_oceanic_phys.F accordingly.
412    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
413    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
414      special setup of gmredi for which the adjoint is stable
415      enough for parameter optimization.
416    o bridging the gap between eddy stress and GM.
417      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
418          along with a change in CPP option (now ALLOW_EDDYPSI).
419      -> when using GM w/ GM_AdvForm:
420          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
421          is applied either in the tracer Eq. or in momentum Eq.
422          depending on data.gmredi (intro. GM_InMomAsStress).
423      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
424      The key modifications are in model/src/taueddy_external_forcing.F
425      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
426    
427    checkpoint59r
428    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
429      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
430      fix option to read coriolis(@ cell-corner) from files with CS-grid.
431    o pkg/mnc: add some attributes to standard 1D-coordinate variables
432    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
433      mass points, when using mnc for output
434      - add runtime parameter (missing_value, missing_value_int) to override
435        default (which is the value of getcon('UNDEF'))
436    o pkg/mnc: prepare mnc for the actual use of missing values with the
437      diagnostics package: small fix in mnc_cw_readwrite.template and more
438      initialisation of never used fields
439      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
440      versions
441    o pkg/thsice/thsice_ini_vars.F added default initial values so that
442      thermodynamics sea ice solver does not blow up when some initial fields
443      are missing.
444    o move from external_forcing_surf.F to ini_forcing.F
445      the p-coord. hack consisting in using pLoad to set phi0surf ;
446      update output of tutorial_global_oce_in_p (affected @ truncation level).
447    o Freshen up a bit hs94.1x64x5, notably:
448      remove rotationPeriod and tRef=5*0. (adjoint only), and add
449      exactConserv=.TRUE.
450    o pkg/generic_advdiff:
451      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
452      applies to files where Temperature & Salinity 2nd Order moments are used.
453    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
454      this uses a dynamically allocated internal state data structure
455      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
456      and requires a fortran 90 compiler
457    
458    checkpoint59q
459    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
460       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
461    o Refresh tutorial_global_oce_biogeo, notably:
462      - change bathymetry (put back seamounts in ACC, use hFacs)
463      - change EOS (POLY3 --> JMD95Z)
464      - use Bryan-Lewis vertical diffusivity
465      - use multidimensional advection
466      - remove old virtual virtual in dic pkg, now done through ptracer pkg
467      - change a couple of parameters in dic pkg
468    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
469    o pkg/obcs: change default to OBCSfixTopo = .true.,
470      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
471      - replace "debugMode" with "debugLevel .GE. debLevB"
472    o implementation of TAF directives for gchem,cfc,dic
473    o remove "exp5" (replaced by tutorial_deep_convection).
474    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
475      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
476      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
477      --> changes results in exp4, seaice_obcs
478    o tutorial_deep_convection :
479      update the set-up and increase resolution and domain size ; start
480      from pseudo initial conditions = output at t=120mn in order to see
481      something happening when running testreport.
482    o pkg/seaice: add os7mp as an advection scheme
483                  add check for advection schemes
484                  add a flag for restoring T and S underneath sea ice
485    o pkg/my82: add netcdf-support and diagnostics
486    o thsice pkg:
487      - Now hsMax limits snow height by turning it into ice following
488        flooding scheme (and now conserving energy)
489      - Slight rewriting of the formula in thsice_calc_thick.F
490      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
491      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
492    
493    checkpoint59p
494    o gchem / dic / cfc :
495      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
496      - add new parameter files: "data.dic" & "data.cfc" ;
497      - various re-arrangement in initialisation & header file ;
498      - fix tutorial_global_oce_biogeo for multi-threaded test.
499    o pkg/dic: test for "pickup_dic" file when restarting ;
500      if no pickup-file, can restart with a re-initialised pH (same as it did
501      before) providing pickupStrictlyMatch is set to False.
502    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
503      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
504    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
505      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
506    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
507     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
508       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
509    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
510       scheme to use for vorticty-term ;
511     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
512       (with default selectVortScheme, return to original discretisation)
513     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
514    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
515    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
516      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
517      also fix diagnostics VISCAHW & VISCA4W.
518    
519    checkpoint59o
520    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
521    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
522      move a few statemens out the main loop into separate loops
523    o pkg/shelfice:
524      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
525        (kg/m^2/s), does not break tests, because in verification/isomip,
526        rhoConstFresh=rhoConst (by accident)
527      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
528      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
529        new file model/src/seawater.F, so that they are available for all pkgs.
530      - convert potential temperature into in-situ temperature. This changes the
531        isomip tests => update tests
532    o add a flag writePickupAtEnd (default=true) to be able to suppress
533      writing a pickup at the last timestep
534    o tools/mpack-1.6 :
535      - disable automake (not working) and autoconf (not needed).
536      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
537        also cleaner with much less compilation warnings.
538    o pkg/profiles:
539      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
540      (for "less than 32 characters name" compiler requirement)
541    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
542      conditions that have a different sampling frequency than S/T/U/V obcs
543    o pkg/diagnostics (stats-diags):
544      - fix global Min/Max in case 1 processor get only empty tiles
545    o genmake2: replace (4 times)
546         make genmake_tc_1.o >> genmake_warnings 2>&1
547      with
548         COMM="$CC $CFLAGS -c genmake_tc_1.c"
549         echo $COMM >> genmake_warnings
550         $COMM >> genmake_warnings 2>&1
551      to make genmake2 always see the value of CC as specified in the optfile.
552    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
553      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
554      - modify verification advect_cs test to test SOM-advection on CS-grid.
555    o pkg/ctrl:
556      - Rewrite of ctrl_map_ini_ecco.F,
557        introducing a generic routine (ctrl_map_ini_gen.F).
558      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
559    
560    checkpoint59n
561    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
562      number in dedicate array "hdiag":
563      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
564        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
565      - many small changes (integer format) for large number of diagnostics
566      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
567        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
568    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
569      usingSphericalGrid, this allows to define the rotated grid coordinates
570      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
571      geographical coordinates according to the inverse of the rotation defined
572      by the Euler angles, so that Coriolis parameter and online-interpolation by
573      exf works with the geographical coordinates on XC/YC/XG/YG.
574      Naturally, this feature does not work with all packages, so some
575      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
576      profiles), because there the coordinates are assumed to be regular
577      spherical grid coordinates.
578    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
579      - introduce isopycnal diffusion coefficient control.
580    o tools/adjoint_options:
581      - additional control vector components.
582    o pkg/mnc: have mnc create marginally meaning full coordinate variables
583      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
584    o pkg/mypackage:
585      - add example of read/write pickup for state-var ;
586      - add entry points to the main code for state-vars diags & write-pickup.
587    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
588      transitions for useExfYearlyFields
589      - add new subroutine that determines the file to read from for
590        use*YearlyFields = .TRUE. and .FALSE.
591      - add a verification experiment to global_with_exf that tests
592        useExfYearlyFields with USE_EXF_INTERPOLATION defined
593    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
594      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
595      subroutines (which could be generated from a template, because they are
596      almost identical), for now they are included in obcs_prescribe_read.F for
597      simplicity
598    o pkg/exf:
599      - add a little more diagnostic to exf_interp_read (in analogy to
600        mds_read_field, can be turned off with debugLevel < debugLevA=1)
601      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
602        ugly but fast by unrolling short inner loops, inserting a unroll=8
603        directive in routine lagran, and splitting a loop and making do while the
604        outermost loop (the latter requires the intoduction of index arrays)
605    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
606    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
607      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
608    o verification/seaice_obcs: updated for restart test and latest options
609    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
610      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
611      for now this is only available for the C-grid code and also within
612      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
613    
614    checkpoint59m
615    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
616      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
617    o gad_som : fix flux output (& diagnostics) to have same units as other  
618      advection scheme fluxes (was previously multiplied by deltaT).  
619    o added verification/seaice_obcs both to test seaice open boundaries
620      and to provide an example matlab scrpt for generating them
621    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
622    o pkg/salt_plume: clean up salt_plume_frac.F to
623      remove redundancy in PlumeMethod 1 and 4
624    o pkg/kpp: added saltplume diagnostics
625    o pkg/obcs and pkg/seaice:
626      - do not set uice and vice to zero when OB*icefile are unspecified
627      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
628      - moved seaice tracer obcs after call to seaice_growth
629    o pkg/salt_plume: added various options for salt plume depth
630      criterion and for vertical distribution of the salt
631    
632    checkpoint59l
633    o pkg/ptracers: new version of ptracers pickup:
634      read meta file and write only fields which are needed to restart.
635      ( same logic as main pickup file ; also using pickupStrictlyMatch )
636    o pkg/seaice:
637      - add timescale for melting due to warm mixed layer as a means of
638        setting SEAICE_availHeatFrac more conveniently
639      - add a CPP-flag/runtime parameter check for flooding algorithm
640      - reformulated availHeat in seaice_growth.F to be independent of AREA
641    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
642      unit changes
643    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
644    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
645      SX vector computer.
646    o pkg/seaice:
647      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
648        seaice forcing fields can now be read only through pkg/exf
649      - removed some unused halos
650    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
651    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
652      or U/VICE from U/VWIND before computing U/VSTRESS
653    
654    checkpoint59k
655    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
656      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
657    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
658      all experiments pass when compile with un-initialised var. checking option.
659    o added pkg/salt_plume
660    o script to test restart (for now, in MITgcm_contrib/jmc_script)
661    o pkg/seaice: new read/write pickup version.
662      read meta file and write only fields which are needed to restart.
663      ( same logic as main pickup file ; also using pickupStrictlyMatch )
664    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
665    o lab_sea.hb87: modify the domain & update output.hb87.txt :
666      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
667      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
668      process. Fixed here by closing the domain at the Northern boundary.
669    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
670    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
671      a set of consecutive levels in/from a 3-D array.
672    o pkg/ptracers:
673      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
674      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
675    
676    checkpoint59j
677    o in pkgs: dic, obcs, offline, rbcs:
678      standard way to compute coeff. for time interpolation between 2 time reccords
679      which retains full precision (& make results less dependent on compiler).
680      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
681    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
682      packages instead of reading ice cover and wind speed separately
683    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
684     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
685      to allow to compile customized code before the update)
686    o cleaning-up:
687      - fix CPP instruction syntax in pkg/obcs
688      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
689        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
690      - fix some threads issue in IO parts.
691    o pkg/dic:
692      - add tons of "_d 0" (--> much better testreports !)
693       and then update outputs of tutorial_global_oce_biogeo
694    o pkg/mom_fluxform:
695      add a special version of momentum advection intended to conserve momentum
696      next to a bathymetry step or a coastline edge. (default = off = #undef)
697    o new read/write pickup version:
698      - for now, only implemented for main (mdsio) pickup file.
699      - write out only what is needed to restart; merge pickup_nh , pickup_ph
700        and main pickup together.
701      - read meta file; read only what is needed to restart; stop if a field
702        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
703        if it make sense (even if the restart is not perfect).
704      - if no meta file, assume that pickup to read corresponds exactly to
705        a pickup that would currently be written.
706      - read pickup written in the old format (until checkpoint59i) if it
707        recognizes an old meta file (no field-list).
708      - add a meta file in exp. which starts from a pickup: 2 cases:
709        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
710         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
711        b) a meta file describing the content of the associated pickup file
712         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
713    o pkg/mdsio & pkg/rw:
714      - new routine to read a meta file ; new set of routine to read
715        Multiple-fields file (with meta file).
716    o added open boundary conditions capability for seaice
717        HSNOW, HSALT, UICE, and VICE
718    
719    checkpoint59i
720    o adjoint:
721      * fix multiDimAdvection adjoint
722        (partial recomputation problem by TAF for fVerT(:,:,kDown)
723        and comlev1 size definition (maxpass vs. max. number of tracers)
724      * verification/global_ocean.90x45x15 adjoint now tests
725        NLFS and multiDimAdvection using DST3 (=30)
726      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
727    o pkg/kpp: add "_d 0" to real constant (if missing);
728      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
729      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
730    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
731      for internal parameters related to restart process (formerly from PARAMS.h)
732      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
733    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
734      as argument. (only atm2d & obcs write_pickup have not yet been updated)
735    o pkg/monitor:
736      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
737      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
738      - account for deep Atmosphere factor and density factor (anelastic)
739    o added open boundary conditions capability for seaice HEFF and AREA
740    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
741      thermodynamics
742      - requires a little reorganization, which affects the testreport results
743        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
744        so that now the conservative form is tested
745      - add a few comments
746    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
747    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
748    o add new diagnostics to seaice: advective, diffusive fluxes (only for
749      multidim-advection, for scheme 2 they are not filled) and transports,
750      thermodynamic growth rates
751    o change units of EmPmR (inside the code, + within coupling interface)
752      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
753      Affects results @ truncation level (cg2d match) and update output of
754       experiments: lab_sea(6), global_ocean.90x40x15(10),
755      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
756      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
757      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
758      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
759    
760    checkpoint59h
761    o pkg/exf:
762      - improve vectorization by moving if-statement out of loops in
763        exf_mapfields, exf_radiation
764      - exf_bulkformulae.F: introduce 2D fields and vectorize code
765    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
766    o testreport:
767      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
768        monitor & update offline_exf_seaice exp. output.
769      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
770    o pkg/seaice:
771      - bug fix in the evp solver: boundary conditions were affected be
772        masking of zMax/zMin (changes results)
773      - minor bug fix in boundary conditions in seaice_calc_strainrates
774        (changes results for no_slip)
775      - seaice_lsr.F: make interpolation of eta dependent on boundaries
776      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
777      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
778        stress formulation and no-slip boundary conditions
779    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
780      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
781    o pkg/seaice: a first HSALT time stepping equation has been checked in
782    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
783      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
784      without requiring DO-IF statements
785    o pkg/thsice:
786      use continuous power-law function for partition of energy between lateral
787      melting/freezing and thinning/thickening ; old code using step function
788      still available with #undef THSICE_FRACEN_POWERLAW
789      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
790    o testreport: change AD testing : check against results/output_adm.txt
791      using same scripts as for forward test.
792    
793    checkpoint59g
794    o adjoint testing: in preparation for changing testreport:
795      - output format: cost and grad written on separated lines
796      - ad output results in directory "results" (instead of "results_ad")
797    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
798    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
799    o pkg/ecco: allow user defined cost function contributions
800    o testreport:
801      Allow to choose (per experiment) the list of tested output variables
802       and the main variable (used to issue a pass/FAIL ) ;
803      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
804      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
805      Also modify printing of summary:
806       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
807       b) echo the list of tested variables in the individual summary.txt of
808          each experiment.
809    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
810      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
811      (but still depend on the tile decompostion of the domain).
812    o pkg/seaice: change a discretization detail to make the B-grid code
813      "more symmetric". This change is likely to remove all "ridges/leads" that
814      where quasi-aligned with the grid in B-grid solutions. It may also be
815      the solution to the stress coupling issues with the B-grid.
816    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
817      remove .cvsignore from input dir. (since testreport no longer run here).
818    o pkg/thsice:
819     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
820     - fix reshaping of sea-ice just after advection:
821       melt all the ice only if ice-volume is too small.
822     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
823       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
824     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
825    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
826      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
827    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
828      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
829      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
830      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
831      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
832      -> update output.txt
833    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
834     this affects truncation error: -> update output.txt of exp:
835      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
836      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
837    
838    checkpoint59f
839    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
840    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
841      a bounded range (in forward mode)
842    o pkg/ecco, ctrl, autodiff and mom_common:
843     internal parameter controls, completements of implementations
844    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
845    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
846      (not seem any difference in testing results).
847    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
848       at face corners.
849    o pkg/generic_advdiff:
850     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
851      loop range indices for computing vertical advection tendency
852      and do the calculation in the interior only (no overlap) ;
853      for now, only implemented for SOM advection (to save CPU time).
854     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
855    o exch2 adjoint
856      First set of changes:
857      - add exch2 hand-written adjoint templates
858      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
859        This will require cleanup in pkg/autodiff/*.F
860        (changed routines currently kept separate in verif. code/)
861      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
862        that used to hide exch2 or cubed-sphere specific code
863        (commented via 'cph-exch2')
864    o pkg/seaice
865      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
866    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
867       output of global_ocean.cs32x15.thsice .
868    
869    checkpoint59e
870    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
871      for B-grid vector (not yet tested) and C-grid vector (<- only used
872      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
873    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
874      (#ifdef ALLOW_SALT_PLUME)
875    o gather_2d/scatter_2d: removed halo regions
876    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
877      scheme and the corresponding test case (under front_relax dir). For now,
878      only available with Skew-flux form and not yet tested in realistic set-up.
879      adjoint: store directives updated, but gradient checks deteriorated,
880      so maybe GM/Redi adjoint is now broken.
881    o seaice adjoint
882      * add AREA, HEFF, HSNOW as control variable
883        (should not change lab_sea results)
884      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
885    o pkg/seaice:
886      * added computation of saltFlux in seaice_growth;
887        For time being, sea ice salinity is assumed constant
888        contribution of snow flooding to freshening of sea ice is neglected.
889        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
890        defaults to 0.0 in order to maintain backward compatibility.
891        Typical values for SEAICE_salinity are 4 to 10 g/kg.
892      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
893      * added SEAICE_availHeatFrac, which specifies fraction of surface level
894        heat content used to melt or grow ice
895      * commented out cap of HICE: it helps keep ice thinner
896      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
897      * applied OBCS T/S mask to HEFFM sea ice mask
898    
899    checkpoint59d
900    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
901     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
902     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
903    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
904     and change default value of parameter "GM_Small_Number";
905     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
906       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
907       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
908    o pkg/ecco: cost function when applying pkg/smooth to controls
909    o pkg/ctrl: add forcingPrecond run time parameter
910    o pkg/seaice:
911     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
912     - fix bug in metric terms of u-equation in LSR solver (implicit part),
913       changes verification/lab_sea
914     - rearrange implicit part of u-equation in LSR solver to make it easier to
915       read, understand, and debug. This causes changes at the truncation level.
916     - fix (serious) bug in the boundary conditions (sign error in the implicit
917       part) of the LSR solver. Changes all LSR results.
918     - fixed problem with HSNOW initialization to avoid thick snow when AREA
919       is initilized with small values - does not change lab_sea results.
920     - added HsnowFile initialization capability
921    o pkg/smooth: addition to model/src and pkg/ctrl so allow
922     initialization of pkg/smooth and application to control vector
923    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
924    o dependencies: pkg/profiles requires pkg/cal
925    o pkg/profiles:
926     - added option ALLOW_PROFILES_GENERICGRID
927         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
928         that interpolation information (grid points and coefficients) is provided
929         within the netcdf input files.
930         -> sample matlab scripts can be found in MITgcm_contrib/gael
931         that allow you to prepare netcdf input files.
932     - also modified: cleaner include statements, cleaner error print statements,
933       cleaner stops when error, and more tests of the netcdf input files consistency.
934    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
935    o pkg/seaice:
936     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
937       requires a new routine: seaice_diagnostics_fill.F
938     - make sure that seaice does not move if not forced (pressure replacement
939       method, Hibler and Ip, 1995), changes results
940     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
941     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
942       It is turned off by default (=-1.), because it changes the results.
943     - make it possible to read AREA from a file, too.
944    
945    checkpoint59c
946    o add S/R and diagnostics for oceanic mixed-layer depth
947    o move GMRedi call after all vertical mixing schemes (including KPP)
948    o pkg/thsice:
949     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
950      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
951    o pkg/obcs:
952     - bug fix for balance code
953    o pkg/seaice:
954      - allow values of SEAICE_elasticParm > 1
955      - add new parameter SEAICE_evpTauRelax as an alternative
956        to SEAICE_elasticParm
957      - make lsr boundary conditions free slip (by default), changes result
958      - add code for no slip boundary conditions for lsr
959      - set minimum of zeta to zero (and not 4e8) (changes results)
960      - add a cap on AREA after advecting AREA if seaice_growth is not called
961    o change calculation of Visbeck K:
962      - no longer depend on tapering scheme; instead, compute slope (limited
963        by GM_maxSlope). this is equivalent to what was comuted before with
964        clipping or linear tappering.
965      - fix vertical averaging (wrong by 1/2 level)
966      - leave the old version (but will not be maintained) within
967        #ifdef OLD_VISBECK_CALC / #endif
968      - update output of exp. ideal_2D_oce
969    o change error catch in calc_r_star to improve vectorization
970    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
971      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
972    o adjoint:
973      Re-organized adjoint checkpointing according to Matt Mazloff
974      (but with modifs/completions/cleanups)
975      Storing is now bundled into large arrays to optimized I/O
976      (and second step in cleanup of the_main_loop)
977    
978    checkpoint59b
979    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
980      - export/import (between ocean & coupler) fields needed for ocean DIC.
981    o pkg/seaice:
982      - get rid of three more exchanges seaice_calc_viscosities (required
983        different loop boundaries in seaice_lsr and seaice_ocean_stress)
984      - bug fix in seaice_ocean_stress (update of lab_sea required)
985      - reduce loop boundaries to necessary minimum also in seaice_evp
986      - go back to the old way of computing deltaC/Z as the adjoint likes that
987        better
988    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
989      passive tracer to an Age Tracer) + update output.txt
990    o pkg/exf:
991      - implement A-grid / C-grid selection for wind-stress input files.
992      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
993      for now, in exf_bulk_largeyeager04.F only :
994      - change implementation for case where windspeed + 2. components wind-stress
995        are read-in. AND use rhoConstFresh to convert evap.
996    o pkg/seaice:
997      - use correct EXCH_UV for wind-forcing (on A-grid).
998      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
999        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
1000    o pkg/exf:
1001      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
1002      EXF_INTERPOLATION:
1003      - merge global_with_exf/code version of exf_interp_read.F
1004        to the main code ;
1005      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
1006        reading the file ; Important: This options needs to be defined to recover
1007        previous code.
1008        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
1009      - no longer loose real*8 precision along the way when using exf_iprec=64.
1010    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
1011      - change discretisation of evp-solver in order to avoid another exchange
1012        (changes lab_sea) and clean up a little
1013      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
1014        help the adjoint (this also changes the results slightly)
1015      - add a few "_d 0" where they had been missing in seaice_evp.F
1016      - cleaning up: remove unused seaice_calc_rhs.F
1017    o pkg/exf: some cleaning-up:
1018      - change various "constants" into runtime parameters
1019      - cleaned-up Large&Yeager04 routine which should eventually
1020        replace exf_bulkformulae.F (changed names of S/R and CPP)
1021        and merged various ALLOW_ATM_WIND options
1022     only used with thsice pkg (in thsice_get_exf.F):
1023      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1024        which are used when useStabilityFct_overIce=TRUE (= the default)
1025      - change default values of ice & snow emissivity and scale downward LW
1026        by ice & snow emissivity.
1027    o pkg/thsice:
1028     fix few little problems, in thsice_calc_thickn.F:
1029      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1030      - melt only laterally if hIce < hThinIce (as the comments say)
1031      and in thsice_extend.F:
1032      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1033      - start to form ice as soon as the minimum ice-volume is reachable.
1034     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1035      and cpl_aim+ocn
1036  o pkg/kpp  o pkg/kpp
  - remove wrong (within bi,bj loops) EXCH calls.  
  - little cleaning (add argument myThid in last position, cvs header ...)  
1037   - move computation of surface related input fields to KPP into a new   - move computation of surface related input fields to KPP into a new
1038     subroutine kpp_forcing_surf.F     subroutine kpp_forcing_surf.F
1039     - remove wrong (within bi,bj loops) EXCH calls.
1040     - little cleaning (add argument myThid in last position, cvs header ...)
1041     - for now, fix conservation problem by exchanging KPPviscAz (may not
1042       be the best fix)
1043  o pkg/seaice  o pkg/seaice
1044   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
1045   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
1046    o OpenAD
1047     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1048    
1049  checkpoint59a  checkpoint59a
1050  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
# Line 31  o in FFIELDS.h: Line 1064  o in FFIELDS.h:
1064       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1065  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1066  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1067      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1068        are no longer updating the vertical diffusivity array
1069        (passed as argument) but are (re-) setting those arrays.
1070  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1071    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1072      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1513  o add two new packages Line 2548  o add two new packages
2548    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2549    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2550      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2551      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2552  o add offline package  o add offline package
2553  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2554    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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