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revision 1.760 by jmc, Sun Dec 24 22:30:57 2006 UTC revision 1.1101 by jmc, Fri May 22 00:25:28 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 SingleCpuIO:
8       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
9    o pkg/seaice:
10       put exchanged variable in (local) common block for MPI+Multi-Threads
11       to work (necessary with exch1, and for now with exch2 too).
12    o verification: to get more experiments tested with mpi, mth and mpi+mth,
13      change tiling of:
14       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
15       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
16      update output of exp:
17       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
18       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
19      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
20                       (note: output.txt generated on faulks using only 1 tile)
21    o eesupp & mdsio (SingleCpuIO):
22     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
23       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
24       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
25     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
26     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
27       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
28    o pkg/exch2:
29     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
30       read parameter file "data.exch2" if it exists; otherwise try default regular
31       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
32     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
33       with new code (not to be used, just as a backup solution).
34     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
35       in utils/exch2/input.
36    
37    checkpoint61n
38    o eesupp & mdsio (SingleCpuIO):
39      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
40        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
41        receive real*4 array (instead of real*8) to read/write 32.bit files.
42        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
43         and remove new mapping S/R)
44    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
45      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
46        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
47        when using exch2. Add S/R to map global io-buffer to global model array.
48      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
49    
50    checkpoint61m
51    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
52      and add 3 other S/R for other types (R4,R8,RS).
53      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
54    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
55     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
56     - reduce number of macro definitions (keep only those which are used);
57       can always call directly the corrresponding S/R if needed.
58     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
59       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
60     Fixed wrong type of arg in:
61       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
62       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
63     To fix: global_sum of var in common block is wrong (multi-threaded) in:
64       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
65     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
66    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
67      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
68    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
69    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
70      edges are closed (zero depth); might happen with "blank tiles";
71      for now, disabled if using OBCS.
72    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
73      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
74    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
75      to reduce length of 1.D array print in STDOUT.
76    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
77      + use 48 tiles (16x8): this will allow to test "blank tiles".
78    o start to test MPI + multi-threaded (change testreport to skip tests
79      where number of tiles do not match).
80    o genmake2: add option "-omp" to turn on Open-MP ;
81      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
82    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
83      and keep the original tile numbering. Note: compatible with old
84      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
85    
86    checkpoint61l
87    o Overlaps had been forgotten in calculating ijk keys : fixed
88    o fix cyrus makedepend for gcc 4.4
89    o experiment fizhi-cs-aqualev20:
90      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
91      and generate new output. Note: new output is much closer to the old
92      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
93      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
94    o pkg/fizhi:
95     - change to avoid indices going deliberately over array-bounds
96     - remove unnecessary MPI stuff
97     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
98     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
99       does not go over array-bounds and therefore returns reliable output.
100     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
101       this S/R has 4 output arguments, which are used inside "get_alarm";
102       when it is called with the same variable "ndum" in place of several
103       output arguments, this produces weird side effect inside "get_alarm"
104      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
105       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
106       address) and produces error.
107    o tools/gemake2: (March 27-29 2009)
108      with option "-mpi": link *_mpi files from "MODS" dir (this is what
109      testreport does).
110    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
111    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
112       update lab_sea.lsr & lab_sea.salt_plume results
113    o pkg/seaice:
114      Major overhaul of the LSOR solver: change discretization from original
115      finite differences to finite volume. The old routine is still in the
116      file seaice_lsr.F and can be turned on with the CPP-flag
117      SEAICE_OLD_AND_BAD_DISCRETIZATION
118      Along with this change, the discretization of the strain rates is changed.
119      The same flag turns on the old discretization in seaice_calc_strainrates.F
120      All verification experiments with seaice are affected (except for
121      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
122      results by setting the above flag.
123      Further changes involve changes in defaults:
124      - ALLOW_FLOODING is defined and turned on by default
125      - SEAICEadvSnow = .true. is now the default
126      - SEAICEadvSalt = .true. is now the default
127      - SEAICEadvAge  = .true. is now the default
128      - SEAICE_clipVelocities  = .false. is now the default
129                                         (as per J. Zhang's recommendation)
130      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
131        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
132      - seaice_growth: replace computation of UG by a simple copy from wspeed
133    
134    checkpoint61k
135    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
136      seaice_lsr: fixed a few metric terms,
137                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
138                  add more debugging diagnostics
139      seaice_evp: removed superfluous many metric terms of FV discretization
140                  of stress divergence
141                  affects lab_sea, lab_sea.hb87
142      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
143                  of stress divergence for non-evp solver
144                  (this part is not tested anywhere)
145      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
146                  they were effectively only half slip
147                  affects lab_sea.hb87
148      updated all relevant verification experiments (except lab_sea//output_adm.txt
149        which was left over, but fails at level 7 & 6)
150    
151    checkpoint61j
152    o pkg/seaice: turn a few hard wired parameters into run time parameters
153    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
154      time in seconds as promised by the usints in seaice_monitor and exf_monitor
155    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
156      that are not cubed-sphere grids
157    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
158    o pkg/ctrl:
159      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
160    o non-hydrostatic (calc_gw.F):
161      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
162      update output of exp. global_ocean.cs32x15.viscA4
163    o remove backward compatibility for thetaMin,phiMin
164      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
165    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
166      interpolated wind field not only for curvilineargrid=.true., but also
167      for a rotated grid (rotateGrid=.true.)
168    o pkg/exf: add capability to bypass interpolation for runoff
169      by setting yet another CPP-flag
170    o eesupp/src, B-grid exchange:
171      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
172    o autodiff
173      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
174      allows to switch to single-prec common blocks;
175      corresponding switch occurs in tamc.h, integer isbyte
176      TAF store directivs "byte" and "kind" seem equivalent;
177      Most tamc.h have been updated correspondingly.
178    
179    checkpoint61i
180    o autodiff:
181      fix autodiff_sore/_restore indices for obcs
182      (spotted by I. Hoteit, M. Mazloff)
183    o pkg/autodiff, pkg/ctrl:
184      Add flag to reduce all tapelev I/O to single-prec.
185      In data.ctrl set
186        doSinglePrecTapelev = .TRUE.
187    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
188      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
189    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
190      real fresh water flux (not yet)
191    o pkg/mdsio & rw:
192     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
193     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
194    o pkg/flt:
195     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
196       init_fixed & ini_varia.
197     - clean-up & simplify linear interpolation S/R:
198       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
199     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
200     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
201     - add vert. coordinate & horiz. indices to output files.
202     - change vertical position in initial condition, from index to depth [m].
203     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
204       (easier to get to a curvilinear grid) ; delX,delY no longer used.
205    o pkg/ggl90: a few modifications:
206     - fix bottom boundary condition, and interpolation of KappaE
207       near top and bottom
208     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
209     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
210     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
211    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
212      (maintain temporary backward compatibility, until next checkpoint)
213    
214    checkpoint61h
215    o pkg/diagnostics with "periodic averaging diagnostics":
216      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
217    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
218    o pkg/obcs: fix loop ranges for balancing code
219    o pkg/flt:
220     - improve criteria for finding which tile owns a float.
221     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
222    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
223      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
224      with ocean biogeo)
225    o pkg/flt:
226     - do some cleaning and fix the restart ;
227     - add output.txt in flt_example/results to get this pkg tested.
228    o genmake2: add an EXTENDED_SRC option and flag.
229       for now, cannot be turned on on command line (only through genmake_local)
230    o pkg/mdsio: read/write vector:
231     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
232     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
233       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
234     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
235      (drop to 4 digits matching for grad). But this test does not look very
236      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
237    
238    checkpoint61g
239    o pkg/flt:
240      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
241       + make OPTIONS file more standard.
242      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
243      - fix _BYTESWAPIO CPP-Flag
244      - standard reading of file-parameter "data.flt"
245      - fix argument list of S/R FLT_RESTART
246      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
247    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
248    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
249      a still unfixed compiler/optimization bug
250    
251    checkpoint61f
252    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
253      update results of global_ocean.cs32x15.icedyn test.
254    o move getcon.F from model/src to pkg/fizhi.
255    o pkg/exf: add parameter for extrapolation of temp up to the surface
256       and option to prevent negative evap (in bulk_largeyeager04 only).
257    o Prather Advection scheme: fix tracer conservation for divergent flow
258      (e.g., when using NonLin Free-Surface).
259    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
260    o gmredi (Visbeck-variable-K):
261     - add more parameters to Visbeck-variable-K.
262     - use a 5 points average for dSigmaR in Visbeck-K calculation
263       (more "homogenous": same stencil and same weights as in dSigmaH)
264     - update output of ideal_2D_oce experiment.
265    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
266      (#undef REAL4_IS_SLOW)
267     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
268       coordinate variable
269     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
270       (surface forcing fields), removes some of the functionality
271     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
272     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
273       probably not all: copy _RS surface flux fields to RL field before
274       calling DIAGNOSTICS_FILL
275     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
276       real*4 (CALL EXCH_*_RS) versions.
277     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
278       (generate new output).
279    
280    checkpoint61e
281    o gmredi (Visbeck-variable-K):
282      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
283      - change computation of Visbeck-K where Slope > Smax :        
284        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
285        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
286    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
287      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
288    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
289    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
290      does not become too large (to avoid precision problems in implicit-diffusion
291      solver); update ideal_2D_oce output.
292    o pkg ggl90:
293      - in ggl90_cal.F: compute only one set of visc/diff, used to
294        step forward TKE/T/S/momentum
295      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
296        have Prandlt =1)
297    o gmredi (fm07):
298      - add lower limit on Transition layer thickness + lower limit on 1/lambda
299      - allow to set few more params from data.gmredi
300    o pkg ggl90:
301          - add missing sqrt(2) factor in computation of mixing length
302            scale in ggl90_calc.F
303            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
304    
305    checkpoint61d
306    o adjoint modifs
307      - adapt to new field rhoInSitu
308      - allow to revert from StoreDynVars2D, StoreDynVars3D
309        to individual fields
310        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
311    o store 3-D (in-situ) density in commom block (DYNVARS.h)
312     - save 1 rho computation.
313     - no longer modify T & S inland when using down_slope pkg.
314    o gad_som : allow to switch to SOM advection for T & S without corresponding
315      pickup files (using new S/R: MDS_CHECK4FILE).
316    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
317      (for useSingleCpuIO to work in multi-threaded)
318    o pkg/shelfice:
319     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
320       with SHELFICEtopoFile in data.shelfice
321     - move code for reading ice shelf topography and modifying hFacC into separate
322       subroutines of the shelfice package
323     - separate initialisation of "fixed" and "variable" variables
324     - kTopC is not (yet) replaced by kSurfC, although this is possible
325    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
326    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
327      and rename:
328      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
329      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
330    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
331    
332    checkpoint61c
333    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
334      to add mass source/sink of fluid in the interior (3-D generalisation
335      of oceanic real-fresh water flux).
336    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
337    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
338    o new pkg: down_slope
339      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
340      - presently, modify T & S inland (dwnslp_calc_rho.F).
341        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
342      - implementation for ocean in P-coords not tested.
343      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
344    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
345      (to facilitate conversion of oceanic pkg to p-coordinate).
346    o change FIND_RHO to FIND_RHO_2D :
347      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
348    o new pkg: cheapaml
349    
350    checkpoint61b
351    o exch2:
352      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
353      - no longer depend on the order sequence (N,S,E,W).
354      - 3rd exchange no longer needed (tested with 24 tiles).
355      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
356      - exch_UV_A-grid readily available (but not yet tested).
357      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
358      (both are no longer needed) in exch_uv: no effect in forward run; but
359       get truncation error differences with adjoint exch.
360    o exch2:
361     - change index-bounds storage (moved from target to local tile,
362       more intuitive this way) ; rename/remove some variables.
363     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
364    
365    checkpoint61a
366    o exch2/matlab-topology-generator:
367      fix bug in index bounds for N-S internal exchange (hard to tell if this
368      had any effect on the solution).
369    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
370      is exceeded
371    o testreport: modify syntax of awk, so that it works also with
372      awk, and not only with nawk and gawk
373    
374    checkpoint61
375    o autodiff
376      Change default for TAF usage by removing argument '-nonew_arg'
377      This changes TAF subroutine argument list (ordering of active var.)
378      Omission of this flag leads to incompatibility w.r.t. TAMC
379      To restore TAMC-compatibility, need following modifs:
380      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
381      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
382      Tested TAF version is 1.9.22
383      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
384    
385    checkpoint60
386    --->>> This is the last checkpoint for which generating the adjoint
387    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
388    --->>> by default.
389    --->>> Future checkpoints will ommit this flag by default.
390    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
391    o pkg/grdchk: Add gradient check to etan0 perturbations.
392    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
393    o pkg/autodiff: more flexibility in zeroadj.
394      model/src: modifying do_oceanic_phys.F accordingly.
395    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
396    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
397      special setup of gmredi for which the adjoint is stable
398      enough for parameter optimization.
399    o bridging the gap between eddy stress and GM.
400      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
401          along with a change in CPP option (now ALLOW_EDDYPSI).
402      -> when using GM w/ GM_AdvForm:
403          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
404          is applied either in the tracer Eq. or in momentum Eq.
405          depending on data.gmredi (intro. GM_InMomAsStress).
406      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
407      The key modifications are in model/src/taueddy_external_forcing.F
408      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
409    
410    checkpoint59r
411    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
412      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
413      fix option to read coriolis(@ cell-corner) from files with CS-grid.
414    o pkg/mnc: add some attributes to standard 1D-coordinate variables
415    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
416      mass points, when using mnc for output
417      - add runtime parameter (missing_value, missing_value_int) to override
418        default (which is the value of getcon('UNDEF'))
419    o pkg/mnc: prepare mnc for the actual use of missing values with the
420      diagnostics package: small fix in mnc_cw_readwrite.template and more
421      initialisation of never used fields
422      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
423      versions
424    o pkg/thsice/thsice_ini_vars.F added default initial values so that
425      thermodynamics sea ice solver does not blow up when some initial fields
426      are missing.
427    o move from external_forcing_surf.F to ini_forcing.F
428      the p-coord. hack consisting in using pLoad to set phi0surf ;
429      update output of tutorial_global_oce_in_p (affected @ truncation level).
430    o Freshen up a bit hs94.1x64x5, notably:
431      remove rotationPeriod and tRef=5*0. (adjoint only), and add
432      exactConserv=.TRUE.
433    o pkg/generic_advdiff:
434      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
435      applies to files where Temperature & Salinity 2nd Order moments are used.
436    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
437      this uses a dynamically allocated internal state data structure
438      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
439      and requires a fortran 90 compiler
440    
441    checkpoint59q
442    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
443       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
444    o Refresh tutorial_global_oce_biogeo, notably:
445      - change bathymetry (put back seamounts in ACC, use hFacs)
446      - change EOS (POLY3 --> JMD95Z)
447      - use Bryan-Lewis vertical diffusivity
448      - use multidimensional advection
449      - remove old virtual virtual in dic pkg, now done through ptracer pkg
450      - change a couple of parameters in dic pkg
451    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
452    o pkg/obcs: change default to OBCSfixTopo = .true.,
453      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
454      - replace "debugMode" with "debugLevel .GE. debLevB"
455    o implementation of TAF directives for gchem,cfc,dic
456    o remove "exp5" (replaced by tutorial_deep_convection).
457    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
458      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
459      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
460      --> changes results in exp4, seaice_obcs
461    o tutorial_deep_convection :
462      update the set-up and increase resolution and domain size ; start
463      from pseudo initial conditions = output at t=120mn in order to see
464      something happening when running testreport.
465    o pkg/seaice: add os7mp as an advection scheme
466                  add check for advection schemes
467                  add a flag for restoring T and S underneath sea ice
468    o pkg/my82: add netcdf-support and diagnostics
469    o thsice pkg:
470      - Now hsMax limits snow height by turning it into ice following
471        flooding scheme (and now conserving energy)
472      - Slight rewriting of the formula in thsice_calc_thick.F
473      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
474      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
475    
476    checkpoint59p
477    o gchem / dic / cfc :
478      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
479      - add new parameter files: "data.dic" & "data.cfc" ;
480      - various re-arrangement in initialisation & header file ;
481      - fix tutorial_global_oce_biogeo for multi-threaded test.
482    o pkg/dic: test for "pickup_dic" file when restarting ;
483      if no pickup-file, can restart with a re-initialised pH (same as it did
484      before) providing pickupStrictlyMatch is set to False.
485    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
486      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
487    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
488      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
489    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
490     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
491       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
492    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
493       scheme to use for vorticty-term ;
494     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
495       (with default selectVortScheme, return to original discretisation)
496     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
497    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
498    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
499      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
500      also fix diagnostics VISCAHW & VISCA4W.
501    
502    checkpoint59o
503    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
504    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
505      move a few statemens out the main loop into separate loops
506    o pkg/shelfice:
507      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
508        (kg/m^2/s), does not break tests, because in verification/isomip,
509        rhoConstFresh=rhoConst (by accident)
510      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
511      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
512        new file model/src/seawater.F, so that they are available for all pkgs.
513      - convert potential temperature into in-situ temperature. This changes the
514        isomip tests => update tests
515    o add a flag writePickupAtEnd (default=true) to be able to suppress
516      writing a pickup at the last timestep
517    o tools/mpack-1.6 :
518      - disable automake (not working) and autoconf (not needed).
519      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
520        also cleaner with much less compilation warnings.
521    o pkg/profiles:
522      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
523      (for "less than 32 characters name" compiler requirement)
524    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
525      conditions that have a different sampling frequency than S/T/U/V obcs
526    o pkg/diagnostics (stats-diags):
527      - fix global Min/Max in case 1 processor get only empty tiles
528    o genmake2: replace (4 times)
529         make genmake_tc_1.o >> genmake_warnings 2>&1
530      with
531         COMM="$CC $CFLAGS -c genmake_tc_1.c"
532         echo $COMM >> genmake_warnings
533         $COMM >> genmake_warnings 2>&1
534      to make genmake2 always see the value of CC as specified in the optfile.
535    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
536      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
537      - modify verification advect_cs test to test SOM-advection on CS-grid.
538    o pkg/ctrl:
539      - Rewrite of ctrl_map_ini_ecco.F,
540        introducing a generic routine (ctrl_map_ini_gen.F).
541      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
542    
543    checkpoint59n
544    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
545      number in dedicate array "hdiag":
546      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
547        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
548      - many small changes (integer format) for large number of diagnostics
549      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
550        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
551    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
552      usingSphericalGrid, this allows to define the rotated grid coordinates
553      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
554      geographical coordinates according to the inverse of the rotation defined
555      by the Euler angles, so that Coriolis parameter and online-interpolation by
556      exf works with the geographical coordinates on XC/YC/XG/YG.
557      Naturally, this feature does not work with all packages, so some
558      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
559      profiles), because there the coordinates are assumed to be regular
560      spherical grid coordinates.
561    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
562      - introduce isopycnal diffusion coefficient control.
563    o tools/adjoint_options:
564      - additional control vector components.
565    o pkg/mnc: have mnc create marginally meaning full coordinate variables
566      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
567    o pkg/mypackage:
568      - add example of read/write pickup for state-var ;
569      - add entry points to the main code for state-vars diags & write-pickup.
570    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
571      transitions for useExfYearlyFields
572      - add new subroutine that determines the file to read from for
573        use*YearlyFields = .TRUE. and .FALSE.
574      - add a verification experiment to global_with_exf that tests
575        useExfYearlyFields with USE_EXF_INTERPOLATION defined
576    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
577      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
578      subroutines (which could be generated from a template, because they are
579      almost identical), for now they are included in obcs_prescribe_read.F for
580      simplicity
581    o pkg/exf:
582      - add a little more diagnostic to exf_interp_read (in analogy to
583        mds_read_field, can be turned off with debugLevel < debugLevA=1)
584      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
585        ugly but fast by unrolling short inner loops, inserting a unroll=8
586        directive in routine lagran, and splitting a loop and making do while the
587        outermost loop (the latter requires the intoduction of index arrays)
588    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
589    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
590      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
591    o verification/seaice_obcs: updated for restart test and latest options
592    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
593      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
594      for now this is only available for the C-grid code and also within
595      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
596    
597    checkpoint59m
598    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
599      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
600    o gad_som : fix flux output (& diagnostics) to have same units as other  
601      advection scheme fluxes (was previously multiplied by deltaT).  
602    o added verification/seaice_obcs both to test seaice open boundaries
603      and to provide an example matlab scrpt for generating them
604    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
605    o pkg/salt_plume: clean up salt_plume_frac.F to
606      remove redundancy in PlumeMethod 1 and 4
607    o pkg/kpp: added saltplume diagnostics
608    o pkg/obcs and pkg/seaice:
609      - do not set uice and vice to zero when OB*icefile are unspecified
610      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
611      - moved seaice tracer obcs after call to seaice_growth
612    o pkg/salt_plume: added various options for salt plume depth
613      criterion and for vertical distribution of the salt
614    
615    checkpoint59l
616    o pkg/ptracers: new version of ptracers pickup:
617      read meta file and write only fields which are needed to restart.
618      ( same logic as main pickup file ; also using pickupStrictlyMatch )
619    o pkg/seaice:
620      - add timescale for melting due to warm mixed layer as a means of
621        setting SEAICE_availHeatFrac more conveniently
622      - add a CPP-flag/runtime parameter check for flooding algorithm
623      - reformulated availHeat in seaice_growth.F to be independent of AREA
624    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
625      unit changes
626    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
627    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
628      SX vector computer.
629    o pkg/seaice:
630      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
631        seaice forcing fields can now be read only through pkg/exf
632      - removed some unused halos
633    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
634    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
635      or U/VICE from U/VWIND before computing U/VSTRESS
636    
637    checkpoint59k
638    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
639      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
640    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
641      all experiments pass when compile with un-initialised var. checking option.
642    o added pkg/salt_plume
643    o script to test restart (for now, in MITgcm_contrib/jmc_script)
644    o pkg/seaice: new read/write pickup version.
645      read meta file and write only fields which are needed to restart.
646      ( same logic as main pickup file ; also using pickupStrictlyMatch )
647    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
648    o lab_sea.hb87: modify the domain & update output.hb87.txt :
649      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
650      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
651      process. Fixed here by closing the domain at the Northern boundary.
652    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
653    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
654      a set of consecutive levels in/from a 3-D array.
655    o pkg/ptracers:
656      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
657      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
658    
659    checkpoint59j
660    o in pkgs: dic, obcs, offline, rbcs:
661      standard way to compute coeff. for time interpolation between 2 time reccords
662      which retains full precision (& make results less dependent on compiler).
663      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
664    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
665      packages instead of reading ice cover and wind speed separately
666    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
667     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
668      to allow to compile customized code before the update)
669    o cleaning-up:
670      - fix CPP instruction syntax in pkg/obcs
671      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
672        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
673      - fix some threads issue in IO parts.
674    o pkg/dic:
675      - add tons of "_d 0" (--> much better testreports !)
676       and then update outputs of tutorial_global_oce_biogeo
677    o pkg/mom_fluxform:
678      add a special version of momentum advection intended to conserve momentum
679      next to a bathymetry step or a coastline edge. (default = off = #undef)
680    o new read/write pickup version:
681      - for now, only implemented for main (mdsio) pickup file.
682      - write out only what is needed to restart; merge pickup_nh , pickup_ph
683        and main pickup together.
684      - read meta file; read only what is needed to restart; stop if a field
685        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
686        if it make sense (even if the restart is not perfect).
687      - if no meta file, assume that pickup to read corresponds exactly to
688        a pickup that would currently be written.
689      - read pickup written in the old format (until checkpoint59i) if it
690        recognizes an old meta file (no field-list).
691      - add a meta file in exp. which starts from a pickup: 2 cases:
692        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
693         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
694        b) a meta file describing the content of the associated pickup file
695         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
696    o pkg/mdsio & pkg/rw:
697      - new routine to read a meta file ; new set of routine to read
698        Multiple-fields file (with meta file).
699    o added open boundary conditions capability for seaice
700        HSNOW, HSALT, UICE, and VICE
701    
702    checkpoint59i
703    o adjoint:
704      * fix multiDimAdvection adjoint
705        (partial recomputation problem by TAF for fVerT(:,:,kDown)
706        and comlev1 size definition (maxpass vs. max. number of tracers)
707      * verification/global_ocean.90x45x15 adjoint now tests
708        NLFS and multiDimAdvection using DST3 (=30)
709      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
710    o pkg/kpp: add "_d 0" to real constant (if missing);
711      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
712      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
713    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
714      for internal parameters related to restart process (formerly from PARAMS.h)
715      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
716    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
717      as argument. (only atm2d & obcs write_pickup have not yet been updated)
718    o pkg/monitor:
719      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
720      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
721      - account for deep Atmosphere factor and density factor (anelastic)
722    o added open boundary conditions capability for seaice HEFF and AREA
723    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
724      thermodynamics
725      - requires a little reorganization, which affects the testreport results
726        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
727        so that now the conservative form is tested
728      - add a few comments
729    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
730    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
731    o add new diagnostics to seaice: advective, diffusive fluxes (only for
732      multidim-advection, for scheme 2 they are not filled) and transports,
733      thermodynamic growth rates
734    o change units of EmPmR (inside the code, + within coupling interface)
735      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
736      Affects results @ truncation level (cg2d match) and update output of
737       experiments: lab_sea(6), global_ocean.90x40x15(10),
738      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
739      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
740      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
741      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
742    
743    checkpoint59h
744    o pkg/exf:
745      - improve vectorization by moving if-statement out of loops in
746        exf_mapfields, exf_radiation
747      - exf_bulkformulae.F: introduce 2D fields and vectorize code
748    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
749    o testreport:
750      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
751        monitor & update offline_exf_seaice exp. output.
752      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
753    o pkg/seaice:
754      - bug fix in the evp solver: boundary conditions were affected be
755        masking of zMax/zMin (changes results)
756      - minor bug fix in boundary conditions in seaice_calc_strainrates
757        (changes results for no_slip)
758      - seaice_lsr.F: make interpolation of eta dependent on boundaries
759      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
760      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
761        stress formulation and no-slip boundary conditions
762    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
763      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
764    o pkg/seaice: a first HSALT time stepping equation has been checked in
765    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
766      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
767      without requiring DO-IF statements
768    o pkg/thsice:
769      use continuous power-law function for partition of energy between lateral
770      melting/freezing and thinning/thickening ; old code using step function
771      still available with #undef THSICE_FRACEN_POWERLAW
772      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
773    o testreport: change AD testing : check against results/output_adm.txt
774      using same scripts as for forward test.
775    
776    checkpoint59g
777    o adjoint testing: in preparation for changing testreport:
778      - output format: cost and grad written on separated lines
779      - ad output results in directory "results" (instead of "results_ad")
780    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
781    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
782    o pkg/ecco: allow user defined cost function contributions
783    o testreport:
784      Allow to choose (per experiment) the list of tested output variables
785       and the main variable (used to issue a pass/FAIL ) ;
786      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
787      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
788      Also modify printing of summary:
789       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
790       b) echo the list of tested variables in the individual summary.txt of
791          each experiment.
792    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
793      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
794      (but still depend on the tile decompostion of the domain).
795    o pkg/seaice: change a discretization detail to make the B-grid code
796      "more symmetric". This change is likely to remove all "ridges/leads" that
797      where quasi-aligned with the grid in B-grid solutions. It may also be
798      the solution to the stress coupling issues with the B-grid.
799    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
800      remove .cvsignore from input dir. (since testreport no longer run here).
801    o pkg/thsice:
802     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
803     - fix reshaping of sea-ice just after advection:
804       melt all the ice only if ice-volume is too small.
805     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
806       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
807     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
808    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
809      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
810    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
811      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
812      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
813      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
814      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
815      -> update output.txt
816    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
817     this affects truncation error: -> update output.txt of exp:
818      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
819      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
820    
821    checkpoint59f
822    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
823    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
824      a bounded range (in forward mode)
825    o pkg/ecco, ctrl, autodiff and mom_common:
826     internal parameter controls, completements of implementations
827    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
828    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
829      (not seem any difference in testing results).
830    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
831       at face corners.
832    o pkg/generic_advdiff:
833     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
834      loop range indices for computing vertical advection tendency
835      and do the calculation in the interior only (no overlap) ;
836      for now, only implemented for SOM advection (to save CPU time).
837     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
838    o exch2 adjoint
839      First set of changes:
840      - add exch2 hand-written adjoint templates
841      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
842        This will require cleanup in pkg/autodiff/*.F
843        (changed routines currently kept separate in verif. code/)
844      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
845        that used to hide exch2 or cubed-sphere specific code
846        (commented via 'cph-exch2')
847    o pkg/seaice
848      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
849    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
850       output of global_ocean.cs32x15.thsice .
851    
852    checkpoint59e
853    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
854      for B-grid vector (not yet tested) and C-grid vector (<- only used
855      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
856    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
857      (#ifdef ALLOW_SALT_PLUME)
858    o gather_2d/scatter_2d: removed halo regions
859    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
860      scheme and the corresponding test case (under front_relax dir). For now,
861      only available with Skew-flux form and not yet tested in realistic set-up.
862      adjoint: store directives updated, but gradient checks deteriorated,
863      so maybe GM/Redi adjoint is now broken.
864    o seaice adjoint
865      * add AREA, HEFF, HSNOW as control variable
866        (should not change lab_sea results)
867      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
868    o pkg/seaice:
869      * added computation of saltFlux in seaice_growth;
870        For time being, sea ice salinity is assumed constant
871        contribution of snow flooding to freshening of sea ice is neglected.
872        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
873        defaults to 0.0 in order to maintain backward compatibility.
874        Typical values for SEAICE_salinity are 4 to 10 g/kg.
875      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
876      * added SEAICE_availHeatFrac, which specifies fraction of surface level
877        heat content used to melt or grow ice
878      * commented out cap of HICE: it helps keep ice thinner
879      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
880      * applied OBCS T/S mask to HEFFM sea ice mask
881    
882    checkpoint59d
883    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
884     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
885     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
886    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
887     and change default value of parameter "GM_Small_Number";
888     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
889       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
890       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
891    o pkg/ecco: cost function when applying pkg/smooth to controls
892    o pkg/ctrl: add forcingPrecond run time parameter
893    o pkg/seaice:
894     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
895     - fix bug in metric terms of u-equation in LSR solver (implicit part),
896       changes verification/lab_sea
897     - rearrange implicit part of u-equation in LSR solver to make it easier to
898       read, understand, and debug. This causes changes at the truncation level.
899     - fix (serious) bug in the boundary conditions (sign error in the implicit
900       part) of the LSR solver. Changes all LSR results.
901     - fixed problem with HSNOW initialization to avoid thick snow when AREA
902       is initilized with small values - does not change lab_sea results.
903     - added HsnowFile initialization capability
904    o pkg/smooth: addition to model/src and pkg/ctrl so allow
905     initialization of pkg/smooth and application to control vector
906    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
907    o dependencies: pkg/profiles requires pkg/cal
908    o pkg/profiles:
909     - added option ALLOW_PROFILES_GENERICGRID
910         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
911         that interpolation information (grid points and coefficients) is provided
912         within the netcdf input files.
913         -> sample matlab scripts can be found in MITgcm_contrib/gael
914         that allow you to prepare netcdf input files.
915     - also modified: cleaner include statements, cleaner error print statements,
916       cleaner stops when error, and more tests of the netcdf input files consistency.
917    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
918    o pkg/seaice:
919     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
920       requires a new routine: seaice_diagnostics_fill.F
921     - make sure that seaice does not move if not forced (pressure replacement
922       method, Hibler and Ip, 1995), changes results
923     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
924     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
925       It is turned off by default (=-1.), because it changes the results.
926     - make it possible to read AREA from a file, too.
927    
928    checkpoint59c
929    o add S/R and diagnostics for oceanic mixed-layer depth
930    o move GMRedi call after all vertical mixing schemes (including KPP)
931    o pkg/thsice:
932     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
933      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
934    o pkg/obcs:
935     - bug fix for balance code
936    o pkg/seaice:
937      - allow values of SEAICE_elasticParm > 1
938      - add new parameter SEAICE_evpTauRelax as an alternative
939        to SEAICE_elasticParm
940      - make lsr boundary conditions free slip (by default), changes result
941      - add code for no slip boundary conditions for lsr
942      - set minimum of zeta to zero (and not 4e8) (changes results)
943      - add a cap on AREA after advecting AREA if seaice_growth is not called
944    o change calculation of Visbeck K:
945      - no longer depend on tapering scheme; instead, compute slope (limited
946        by GM_maxSlope). this is equivalent to what was comuted before with
947        clipping or linear tappering.
948      - fix vertical averaging (wrong by 1/2 level)
949      - leave the old version (but will not be maintained) within
950        #ifdef OLD_VISBECK_CALC / #endif
951      - update output of exp. ideal_2D_oce
952    o change error catch in calc_r_star to improve vectorization
953    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
954      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
955    o adjoint:
956      Re-organized adjoint checkpointing according to Matt Mazloff
957      (but with modifs/completions/cleanups)
958      Storing is now bundled into large arrays to optimized I/O
959      (and second step in cleanup of the_main_loop)
960    
961    checkpoint59b
962    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
963      - export/import (between ocean & coupler) fields needed for ocean DIC.
964    o pkg/seaice:
965      - get rid of three more exchanges seaice_calc_viscosities (required
966        different loop boundaries in seaice_lsr and seaice_ocean_stress)
967      - bug fix in seaice_ocean_stress (update of lab_sea required)
968      - reduce loop boundaries to necessary minimum also in seaice_evp
969      - go back to the old way of computing deltaC/Z as the adjoint likes that
970        better
971    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
972      passive tracer to an Age Tracer) + update output.txt
973    o pkg/exf:
974      - implement A-grid / C-grid selection for wind-stress input files.
975      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
976      for now, in exf_bulk_largeyeager04.F only :
977      - change implementation for case where windspeed + 2. components wind-stress
978        are read-in. AND use rhoConstFresh to convert evap.
979    o pkg/seaice:
980      - use correct EXCH_UV for wind-forcing (on A-grid).
981      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
982        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
983    o pkg/exf:
984      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
985      EXF_INTERPOLATION:
986      - merge global_with_exf/code version of exf_interp_read.F
987        to the main code ;
988      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
989        reading the file ; Important: This options needs to be defined to recover
990        previous code.
991        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
992      - no longer loose real*8 precision along the way when using exf_iprec=64.
993    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
994      - change discretisation of evp-solver in order to avoid another exchange
995        (changes lab_sea) and clean up a little
996      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
997        help the adjoint (this also changes the results slightly)
998      - add a few "_d 0" where they had been missing in seaice_evp.F
999      - cleaning up: remove unused seaice_calc_rhs.F
1000    o pkg/exf: some cleaning-up:
1001      - change various "constants" into runtime parameters
1002      - cleaned-up Large&Yeager04 routine which should eventually
1003        replace exf_bulkformulae.F (changed names of S/R and CPP)
1004        and merged various ALLOW_ATM_WIND options
1005     only used with thsice pkg (in thsice_get_exf.F):
1006      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
1007        which are used when useStabilityFct_overIce=TRUE (= the default)
1008      - change default values of ice & snow emissivity and scale downward LW
1009        by ice & snow emissivity.
1010    o pkg/thsice:
1011     fix few little problems, in thsice_calc_thickn.F:
1012      - growth vertically (and not laterally) if iceFrac == iceMaskMax
1013      - melt only laterally if hIce < hThinIce (as the comments say)
1014      and in thsice_extend.F:
1015      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1016      - start to form ice as soon as the minimum ice-volume is reachable.
1017     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
1018      and cpl_aim+ocn
1019    o pkg/kpp
1020     - move computation of surface related input fields to KPP into a new
1021       subroutine kpp_forcing_surf.F
1022     - remove wrong (within bi,bj loops) EXCH calls.
1023     - little cleaning (add argument myThid in last position, cvs header ...)
1024     - for now, fix conservation problem by exchanging KPPviscAz (may not
1025       be the best fix)
1026    o pkg/seaice
1027     - check for inconsistent evp parameter/cpp-flag combination
1028     - remove leftover errIO flat for obsolete name list error handling
1029    o OpenAD
1030     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
1031    
1032    checkpoint59a
1033    o pkg/seaice: some parameter clarifications and a little bit of clean up
1034    o pkg/thsice: rename run-time parameters:
1035       himin       -> hIceMin
1036       himin0      -> hThinIce
1037       hihig       -> hThickIce
1038       i0          -> i0swFrac
1039       transCoef   -> bMeltCoef
1040       frac_energy -> fracMelting
1041      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
1042       with default values (for now) that do not change the results.
1043      remove old version of thsice vars advection in pkg/seaice.
1044    o in FFIELDS.h:
1045      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
1046      - make pLoad & sIceLoad always available (but still only used if
1047         ATMOSPHERIC_LOADING is #define).
1048    o pkg/kpp: replaced _KPP_RL with _RL
1049    o bug fixes for vertical diffusivity computations when both KPP and
1050        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1051        are no longer updating the vertical diffusivity array
1052        (passed as argument) but are (re-) setting those arrays.
1053    o pkg/seaice: fix bug in evp solver, while doing that
1054      - change (improve?) discretization of stress computations for both
1055        cgrid-lsr and evp solver
1056      - add a new routine to compute strain rates
1057      - the above changes lab_sea results
1058      - add no slip conditions for evp solver (off by default), lsr-version
1059        may follow
1060      - fix exchange for shear at Z-points (does not change lab_sea)
1061      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
1062        (to force the user to pick a time step since there is not "safe" way
1063        of choosing it)
1064      - add principal stress diagnostics
1065      - rearrange fields for evp a little to avoid having to call a: too many
1066        exchanges and b: exchanges for stress trensor components which we do
1067        not have.
1068      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
1069        of evp, complete rewrite for lsr case (latter is does not yet work
1070        in all cases)
1071    o pkg/kpp: add code to have mixing in shelf ice caverns
1072      - add myThid to all kpp routines (long overdue)
1073    
1074    checkpoint59
1075    o pkg/exf:
1076      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
1077        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
1078      - move exf header files from lower_case.h to UPPER_CASE.h ;
1079        add missing cvs Header & Name
1080      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
1081      - add namelist param. selectStressGridPosition, exf_monFreq
1082      - retire many _CLIM routines, and remove data.exf_clim
1083        + params moved to data.exf
1084        + climsst, climsss now handled by exf_set_gen, i.e.
1085          climss?period=0 refers to constant field,
1086          climss?period=-12 to monthly forcing
1087      - split up namelists in data.exf
1088    o pkg/seaice:
1089      - remove seaice_exch and seaice_exch_uv
1090      - remove superfluous exchange of theta
1091      - add myThid to seaice_budget_ocean/ice
1092      - add new interface for atmospheric wind forcing (C-grid only)
1093        + new routine
1094        + two new field (taux, tauy for stress over ice)
1095        + removed one global field (DAIRN) for C-grid case only
1096    o pkg/thsise
1097      - 2nd set of modifs for thsice adjoint in conjunction with exf
1098    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
1099    
1100    checkpoint58y_post
1101    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
1102      vertical diffusivity, similar to that in MOM4; turned on using
1103      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
1104      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
1105    o Added capability for 3D specification of background vertical diffusion
1106      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
1107      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
1108      "data" file that contains the 3D vertical diffusivity coefficients.
1109    o ice dynamics (pkg/seaice) with thsice thermodynamics:
1110      - add code within pkg thsice to advect & diffuse sea-ice fields
1111      similar to (and will replace) what has been added in  seaice_advdiff.F,
1112      but: - conserving Mass, Heat & Salt.
1113           - better when using non-linear advection scheme (not yet fully tested)
1114           - can also be used in atmospheric set-up (for now, only the diffusion).
1115    
1116    checkpoint58x_post
1117    o IO option for global-file compact format:
1118      - add options when generating topology (utils/exch2/matlab-topology-generator)
1119      - add I/O capability (pkg/mdsio).
1120      - adapt utils/matlab/rdmds.m to read this format.
1121      for now long-line format not yet supported by pkg/mdsio (& exch2).
1122    o shelfice: add a few diagnostics
1123    
1124    checkpoint58w_post
1125    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
1126      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
1127      (and replace horiVertRatio in NH code).
1128      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
1129                         and tutorial_plume_on_slope (sensitive to truncation)
1130    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
1131      directly to drive seaice model (C-grid only)
1132    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
1133     - reintroduce computation of wind from stress,
1134     - compute tau (in exf_bulkformulae.F) from windstress averaged to
1135       mass points to avoid tau = 0
1136     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
1137    o rdmnc.m: make it work with "global" files created with gluemnc
1138    o rdmnc.m : some improvements in dealing with singleton dimension
1139      (tested on all testreport mnc output files).
1140    o genmake2: disable pkg/profiles if netcdf test fails.
1141    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
1142    o move call to cal_readparms up to make calendar parameters/variable available
1143      to all packages
1144    
1145    checkpoint58v_post
1146    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
1147      useDynP_inEos_Zc tested.
1148    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1149    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1150      and portions thereof.  See read_cs.txt for description and examples.
1151    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1152      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1153      following the great-circle arc between those 2 points.
1154    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1155      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1156    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1157     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1158     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1159     - still needs work (not working with some options ; efficiency to improve)
1160       and serious testing.
1161     - use this scheme for temperature & salinity in 2 advection test exp.:
1162       advect_xy & advect_xz, respectively.
1163    
1164    checkpoint58u_post
1165    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1166    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1167    o testreport: add option "-skipdir" to skip some test.
1168    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1169      momentum calculation.
1170    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1171    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1172      remove checkpoint.F and the_correction_step.F (no longer used);
1173      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1174    o add option (linFSConserveTr) to correct for tracer source/sink due to
1175      Linear Free surface
1176    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1177    o pkg/thsice: fix reading mnc-pickups
1178    
1179    checkpoint58t_post
1180    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1181    o pkg/mdsio:
1182     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1183       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1184       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1185     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1186     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1187       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1188     - new S/R (to replace MDSWRITEMETA), which allows to write more
1189       informations (variable names, time ...) to meta files.
1190     - modify rdmds.m to give back the meta file content.
1191  o pkg/diagnostics: change vertical interpolation to be safer, and more  o pkg/diagnostics: change vertical interpolation to be safer, and more
1192     flexible (define p-levels to interpolate to in data.diagnostics);     flexible (define p-levels to interpolate to in data.diagnostics);
1193    add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right    add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1194     diagnostic pointer.     diagnostic pointer.
1195  o pkg/seaice: more cleaning up of seaice_growth, added many comments  o pkg/seaice: more cleaning up of seaice_growth, added many comments
1196  o pkg/exf: put runoff0 and runoff into the appropriate common block  o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1197  o fix multi-category seaice:  o fix multi-category seaice:
1198   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:   - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1199     SEAICE_MULTICATEGORY     SEAICE_MULTICATEGORY
# Line 1347  o add two new packages Line 2531  o add two new packages
2531    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2532    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2533      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2534      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2535  o add offline package  o add offline package
2536  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2537    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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