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

Diff of /MITgcm/doc/tag-index

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

revision 1.826 by mlosch, Fri Jun 1 12:57:48 2007 UTC revision 1.1159 by jmc, Mon Sep 21 15:50:14 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61v
8    o pkg/kpp:
9     -add double diffusive contributions as a hack, turned off by default
10      for now, and the code can be excluded with a CPP-flag
11      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
12     -add a verification experiments to "vermix" to test this code
13    o pkg/mom_common:
14      Move computation of length scales to mom_init_fixed.F (avoid recomputation
15      at each time-steps*levels).
16    o pkg/layers:
17      Created a new package for computing volume fluxes in temperature or
18      [not yet implemented] density layers, e.g. for calculating residual
19      overturning circulations.
20    o pkg/diagnostics:
21      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
22    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
23    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
24      To avoid mixing type (RS/RL) of input/output array argument,
25      replace single mixed-type array with a pair from each type (RS/RL).
26    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
27      is now implemented for all pkgs (previously only done for the main pickup)
28    
29    checkpoint61u
30    o pkg/obcs:
31      - change OB?eta from _RS to _RL and put them into a separate commen block
32      - add code to read OB?eta from a file via obcs_prescribe_read: the code
33        compiles and does not destroy any other experiments, the data is read
34        properly, but the code is not tested in actual applications
35    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
36      create a meaningful unit attribute for the time coordinate variable
37    o pkg/ebm: add plenty of missing "_d 0" ;
38       update results of experiment global_ocean_ebm (fwd + adjoint tests)
39      Notes: several pieces of code only works for (very) specific set up
40       (domain size, lat range, etc ...); should be documented & stop if one
41       of those assumptions is not meet.
42    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
43       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
44          and offline_exf_seaice (seaicetd + adjoint).
45    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
46       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
47        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
48    o few changes to pass when compiling with strick checking of arguments
49       across S/R (allow to find few bugs in S/R calls).
50    o pkg/seaice:
51     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
52       2d-fields, for slightly better performance
53    
54    checkpoint61t
55    o pkg/seaice:
56     - remove unused variables in seaice_evp
57     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
58    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
59       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
60       each processor opens a different file (a fix from Matt).
61    o cg2d:
62       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
63       this reduces number of EXCH calls by 2 when using exch2.
64       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
65       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
66    o pkg/thsice:
67       add code for Near Infra-Red albedo (from Jeff)
68       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
69    o ini_model_io:
70       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
71       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
72       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
73    
74    checkpoint61s
75    o pkg/exch2 (exch2_rxN_cube*):
76       remove last BARRIER (no need to synchronise after getting data from shared
77       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
78    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
79      and generate new output (for the 2 tests) using default rotationPeriod.
80    o pkg/exch2:
81      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
82        (was already the case with AUTODIFF_EXCH2 defined)
83      - add bj in exch2 arrays and S/R.
84      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
85        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
86    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
87      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
88        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
89      - verification experiment natl_box.longstep
90    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
91      allow different versions of ifort (8 or 9) and different versions
92       of mpi (mpich or mpich2) to be used with the same optfile.
93      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
94       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
95    o pkg/seaice:
96      fix previous modif (3-level field removed) for old-pickup reading
97    
98    checkpoint61r
99    o pkg/seaice:
100     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
101      1. introduce fields for time step (N-1)
102      2. do not use levels 2 and 3 anymore (but keep them)
103      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
104         includes changes to pkg/thsice/thsice_get_velocity.F,
105         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
106         pkg/obcs/obcs_apply_uvice.F.
107     - completely remove code for leap-frog time stepping for second order
108       advection
109     - adjusted adjoint accordingly;
110       gradient checks have improved by an order of magnitude!
111    
112    checkpoint61q
113    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
114     - the boundary conditions along open boundaries are unclear, because the
115       associated masks are set to zero and are thus treated as closed when
116       applying the slip-boundary conditions.
117     - move initialisation of grid variables from seaice_init_varia to _fixed
118    o adding doc/diags_changes.txt
119    o model/src:
120      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
121       to avoid "_diags" naming if no relation to pkg/diagnostics.
122      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
123       file and only call PLOT_FIELD_XYZ if debugMode=T.
124      remove few PLOT_FIELD_XY calls outside initialisation.
125      remove few unnecessary BARRIER.
126    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
127      of salt_plume package in Southern Ocean
128    o pkg/thsice:
129     - fix hOceMxL in overlap (needed for sea-ice advection);
130       update output of experiment global_ocean.cs32x15.icedyn.
131    o pkg/seaice:
132     - make the (placeholder-)tracer IceAge a little more meaningful
133      by avoiding ridging of age due to convergent ice flow
134     - add diagnostics for surface temperature, atmospheric and oceanic
135       heat flux, and atmospheric and oceanic ice growth
136    
137    checkpoint61p
138    o eesupp (global_max & global_sum):
139     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
140     - remove starting & endding barrier (no longer needed)
141    o pkg/mdsio, writelocal:
142       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
143       (remove the STOP): uses shared buffer IO to store data from all threads
144       and then let master-thread write nThreads tiles.
145    o pkg/mdsio (read/write field):
146     - tiled IO done in 1 piece (all levels at a time);
147     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
148     - multi-threaded: allow to read/write local (non-shared) array
149       (was already working with singleCpuIO ; now works also without);
150       => no longer needs barrier call after reading a file (added inside
151       mds_read/write field).
152     - move barrier calls outside gather/scatter_2d to mds_read/write_field
153    o pkg/obcs/exf
154      - exf_getffieldrec.F: add a few ". _d 0" and
155                            add code to catch the case fldperiod = 0.  
156      - obcs_precribe_read.F: change if statements so that they match
157                              the variable type (_RL)
158      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
159        exf_iprec) as part of namelist EXF_NML_01
160    o pkg/mdsio:
161      - read/write tiled (local) files: read/write 1-level tile chunk at a time
162        (instead of segment of length sNx); expected to speed up tiled IO.
163    o pkg/exch2:
164      - take buffer copy from/to array out of S/R exch2_send/recv into new
165        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
166        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
167      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
168      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
169        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
170        including Topology header file (and common blocks).
171      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
172        remove 2nd exch call in exch2_s3d_rx (no longer needed).
173      - document S/R arg. list (+ update some comments)
174    o pkg/seaice:
175      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
176        temperature and humidity over sea ice based on climatological values.
177      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
178        of LSR (this change is expected to change the results slightly because now
179        it uses slightly difference moduli from the second last LSR solution, but
180        that is more consistent with the stress computations; this part of the code
181        is not tested in the verification experiments)
182      - fix diagnostics for flux of ice in case of B-grid
183      - turn strain rates eij and press into global fields within global
184        common block in SEAICE.h for more straighforward diagnostics
185      - fix diagnostics for principal stress components, press, zeta, eta
186        to give something meaning full
187    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
188      new output (all 4 tests) using default rotationPeriod.
189    o pkg KPP:
190      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
191      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
192        and normal grid from 1 to Nr)
193    o Fix computations of L4rdt in mom_calc_visc.F
194    o eesupp:
195      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
196      should be called before a "stop" if we know that all process are going
197      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
198    
199    checkpoint61o
200    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
201    o model/src/ini_curvilinear_grid.F:
202       compute angleSin/CosC when they are not read from a file
203    o pkg/seaice:
204       add pseudo time stepping for LSOR
205    o pkg/exch2:
206       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
207    o pkg/seaice:
208       Adding separate sea ice albedo, drag coefficients, and HO in Southern
209       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
210    o SingleCpuIO:
211       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
212    o pkg/seaice:
213       put exchanged variable in (local) common block for MPI+Multi-Threads
214       to work (necessary with exch1, and for now with exch2 too).
215    o verification: to get more experiments tested with mpi, mth and mpi+mth,
216      change tiling of:
217       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
218       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
219      update output of exp:
220       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
221       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
222      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
223                       (note: output.txt generated on faulks using only 1 tile)
224    o eesupp & mdsio (SingleCpuIO):
225     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
226       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
227       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
228     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
229     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
230       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
231    o pkg/exch2:
232     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
233       read parameter file "data.exch2" if it exists; otherwise try default regular
234       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
235     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
236       with new code (not to be used, just as a backup solution).
237     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
238       in utils/exch2/input.
239    
240    checkpoint61n
241    o eesupp & mdsio (SingleCpuIO):
242      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
243        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
244        receive real*4 array (instead of real*8) to read/write 32.bit files.
245        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
246         and remove new mapping S/R)
247    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
248      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
249        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
250        when using exch2. Add S/R to map global io-buffer to global model array.
251      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
252    
253    checkpoint61m
254    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
255      and add 3 other S/R for other types (R4,R8,RS).
256      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
257    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
258     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
259     - reduce number of macro definitions (keep only those which are used);
260       can always call directly the corrresponding S/R if needed.
261     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
262       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
263     Fixed wrong type of arg in:
264       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
265       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
266     To fix: global_sum of var in common block is wrong (multi-threaded) in:
267       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
268     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
269    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
270      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
271    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
272    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
273      edges are closed (zero depth); might happen with "blank tiles";
274      for now, disabled if using OBCS.
275    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
276      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
277    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
278      to reduce length of 1.D array print in STDOUT.
279    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
280      + use 48 tiles (16x8): this will allow to test "blank tiles".
281    o start to test MPI + multi-threaded (change testreport to skip tests
282      where number of tiles do not match).
283    o genmake2: add option "-omp" to turn on Open-MP ;
284      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
285    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
286      and keep the original tile numbering. Note: compatible with old
287      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
288    
289    checkpoint61l
290    o Overlaps had been forgotten in calculating ijk keys : fixed
291    o fix cyrus makedepend for gcc 4.4
292    o experiment fizhi-cs-aqualev20:
293      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
294      and generate new output. Note: new output is much closer to the old
295      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
296      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
297    o pkg/fizhi:
298     - change to avoid indices going deliberately over array-bounds
299     - remove unnecessary MPI stuff
300     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
301     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
302       does not go over array-bounds and therefore returns reliable output.
303     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
304       this S/R has 4 output arguments, which are used inside "get_alarm";
305       when it is called with the same variable "ndum" in place of several
306       output arguments, this produces weird side effect inside "get_alarm"
307      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
308       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
309       address) and produces error.
310    o tools/gemake2: (March 27-29 2009)
311      with option "-mpi": link *_mpi files from "MODS" dir (this is what
312      testreport does).
313    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
314    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
315       update lab_sea.lsr & lab_sea.salt_plume results
316    o pkg/seaice:
317      Major overhaul of the LSOR solver: change discretization from original
318      finite differences to finite volume. The old routine is still in the
319      file seaice_lsr.F and can be turned on with the CPP-flag
320      SEAICE_OLD_AND_BAD_DISCRETIZATION
321      Along with this change, the discretization of the strain rates is changed.
322      The same flag turns on the old discretization in seaice_calc_strainrates.F
323      All verification experiments with seaice are affected (except for
324      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
325      results by setting the above flag.
326      Further changes involve changes in defaults:
327      - ALLOW_FLOODING is defined and turned on by default
328      - SEAICEadvSnow = .true. is now the default
329      - SEAICEadvSalt = .true. is now the default
330      - SEAICEadvAge  = .true. is now the default
331      - SEAICE_clipVelocities  = .false. is now the default
332                                         (as per J. Zhang's recommendation)
333      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
334        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
335      - seaice_growth: replace computation of UG by a simple copy from wspeed
336    
337    checkpoint61k
338    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
339      seaice_lsr: fixed a few metric terms,
340                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
341                  add more debugging diagnostics
342      seaice_evp: removed superfluous many metric terms of FV discretization
343                  of stress divergence
344                  affects lab_sea, lab_sea.hb87
345      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
346                  of stress divergence for non-evp solver
347                  (this part is not tested anywhere)
348      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
349                  they were effectively only half slip
350                  affects lab_sea.hb87
351      updated all relevant verification experiments (except lab_sea//output_adm.txt
352        which was left over, but fails at level 7 & 6)
353    
354    checkpoint61j
355    o pkg/seaice: turn a few hard wired parameters into run time parameters
356    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
357      time in seconds as promised by the usints in seaice_monitor and exf_monitor
358    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
359      that are not cubed-sphere grids
360    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
361    o pkg/ctrl:
362      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
363    o non-hydrostatic (calc_gw.F):
364      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
365      update output of exp. global_ocean.cs32x15.viscA4
366    o remove backward compatibility for thetaMin,phiMin
367      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
368    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
369      interpolated wind field not only for curvilineargrid=.true., but also
370      for a rotated grid (rotateGrid=.true.)
371    o pkg/exf: add capability to bypass interpolation for runoff
372      by setting yet another CPP-flag
373    o eesupp/src, B-grid exchange:
374      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
375    o autodiff
376      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
377      allows to switch to single-prec common blocks;
378      corresponding switch occurs in tamc.h, integer isbyte
379      TAF store directivs "byte" and "kind" seem equivalent;
380      Most tamc.h have been updated correspondingly.
381    
382    checkpoint61i
383    o autodiff:
384      fix autodiff_sore/_restore indices for obcs
385      (spotted by I. Hoteit, M. Mazloff)
386    o pkg/autodiff, pkg/ctrl:
387      Add flag to reduce all tapelev I/O to single-prec.
388      In data.ctrl set
389        doSinglePrecTapelev = .TRUE.
390    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
391      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
392    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
393      real fresh water flux (not yet)
394    o pkg/mdsio & rw:
395     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
396     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
397    o pkg/flt:
398     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
399       init_fixed & ini_varia.
400     - clean-up & simplify linear interpolation S/R:
401       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
402     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
403     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
404     - add vert. coordinate & horiz. indices to output files.
405     - change vertical position in initial condition, from index to depth [m].
406     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
407       (easier to get to a curvilinear grid) ; delX,delY no longer used.
408    o pkg/ggl90: a few modifications:
409     - fix bottom boundary condition, and interpolation of KappaE
410       near top and bottom
411     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
412     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
413     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
414    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
415      (maintain temporary backward compatibility, until next checkpoint)
416    
417    checkpoint61h
418    o pkg/diagnostics with "periodic averaging diagnostics":
419      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
420    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
421    o pkg/obcs: fix loop ranges for balancing code
422    o pkg/flt:
423     - improve criteria for finding which tile owns a float.
424     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
425    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
426      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
427      with ocean biogeo)
428    o pkg/flt:
429     - do some cleaning and fix the restart ;
430     - add output.txt in flt_example/results to get this pkg tested.
431    o genmake2: add an EXTENDED_SRC option and flag.
432       for now, cannot be turned on on command line (only through genmake_local)
433    o pkg/mdsio: read/write vector:
434     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
435     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
436       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
437     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
438      (drop to 4 digits matching for grad). But this test does not look very
439      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
440    
441    checkpoint61g
442    o pkg/flt:
443      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
444       + make OPTIONS file more standard.
445      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
446      - fix _BYTESWAPIO CPP-Flag
447      - standard reading of file-parameter "data.flt"
448      - fix argument list of S/R FLT_RESTART
449      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
450    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
451    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
452      a still unfixed compiler/optimization bug
453    
454    checkpoint61f
455    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
456      update results of global_ocean.cs32x15.icedyn test.
457    o move getcon.F from model/src to pkg/fizhi.
458    o pkg/exf: add parameter for extrapolation of temp up to the surface
459       and option to prevent negative evap (in bulk_largeyeager04 only).
460    o Prather Advection scheme: fix tracer conservation for divergent flow
461      (e.g., when using NonLin Free-Surface).
462    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
463    o gmredi (Visbeck-variable-K):
464     - add more parameters to Visbeck-variable-K.
465     - use a 5 points average for dSigmaR in Visbeck-K calculation
466       (more "homogenous": same stencil and same weights as in dSigmaH)
467     - update output of ideal_2D_oce experiment.
468    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
469      (#undef REAL4_IS_SLOW)
470     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
471       coordinate variable
472     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
473       (surface forcing fields), removes some of the functionality
474     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
475     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
476       probably not all: copy _RS surface flux fields to RL field before
477       calling DIAGNOSTICS_FILL
478     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
479       real*4 (CALL EXCH_*_RS) versions.
480     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
481       (generate new output).
482    
483    checkpoint61e
484    o gmredi (Visbeck-variable-K):
485      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
486      - change computation of Visbeck-K where Slope > Smax :        
487        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
488        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
489    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
490      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
491    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
492    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
493      does not become too large (to avoid precision problems in implicit-diffusion
494      solver); update ideal_2D_oce output.
495    o pkg ggl90:
496      - in ggl90_cal.F: compute only one set of visc/diff, used to
497        step forward TKE/T/S/momentum
498      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
499        have Prandlt =1)
500    o gmredi (fm07):
501      - add lower limit on Transition layer thickness + lower limit on 1/lambda
502      - allow to set few more params from data.gmredi
503    o pkg ggl90:
504          - add missing sqrt(2) factor in computation of mixing length
505            scale in ggl90_calc.F
506            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
507    
508    checkpoint61d
509    o adjoint modifs
510      - adapt to new field rhoInSitu
511      - allow to revert from StoreDynVars2D, StoreDynVars3D
512        to individual fields
513        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
514    o store 3-D (in-situ) density in commom block (DYNVARS.h)
515     - save 1 rho computation.
516     - no longer modify T & S inland when using down_slope pkg.
517    o gad_som : allow to switch to SOM advection for T & S without corresponding
518      pickup files (using new S/R: MDS_CHECK4FILE).
519    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
520      (for useSingleCpuIO to work in multi-threaded)
521    o pkg/shelfice:
522     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
523       with SHELFICEtopoFile in data.shelfice
524     - move code for reading ice shelf topography and modifying hFacC into separate
525       subroutines of the shelfice package
526     - separate initialisation of "fixed" and "variable" variables
527     - kTopC is not (yet) replaced by kSurfC, although this is possible
528    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
529    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
530      and rename:
531      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
532      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
533    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
534    
535    checkpoint61c
536    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
537      to add mass source/sink of fluid in the interior (3-D generalisation
538      of oceanic real-fresh water flux).
539    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
540    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
541    o new pkg: down_slope
542      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
543      - presently, modify T & S inland (dwnslp_calc_rho.F).
544        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
545      - implementation for ocean in P-coords not tested.
546      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
547    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
548      (to facilitate conversion of oceanic pkg to p-coordinate).
549    o change FIND_RHO to FIND_RHO_2D :
550      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
551    o new pkg: cheapaml
552    
553    checkpoint61b
554    o exch2:
555      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
556      - no longer depend on the order sequence (N,S,E,W).
557      - 3rd exchange no longer needed (tested with 24 tiles).
558      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
559      - exch_UV_A-grid readily available (but not yet tested).
560      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
561      (both are no longer needed) in exch_uv: no effect in forward run; but
562       get truncation error differences with adjoint exch.
563    o exch2:
564     - change index-bounds storage (moved from target to local tile,
565       more intuitive this way) ; rename/remove some variables.
566     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
567    
568    checkpoint61a
569    o exch2/matlab-topology-generator:
570      fix bug in index bounds for N-S internal exchange (hard to tell if this
571      had any effect on the solution).
572    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
573      is exceeded
574    o testreport: modify syntax of awk, so that it works also with
575      awk, and not only with nawk and gawk
576    
577    checkpoint61
578    o autodiff
579      Change default for TAF usage by removing argument '-nonew_arg'
580      This changes TAF subroutine argument list (ordering of active var.)
581      Omission of this flag leads to incompatibility w.r.t. TAMC
582      To restore TAMC-compatibility, need following modifs:
583      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
584      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
585      Tested TAF version is 1.9.22
586      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
587    
588    checkpoint60
589    --->>> This is the last checkpoint for which generating the adjoint
590    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
591    --->>> by default.
592    --->>> Future checkpoints will ommit this flag by default.
593    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
594    o pkg/grdchk: Add gradient check to etan0 perturbations.
595    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
596    o pkg/autodiff: more flexibility in zeroadj.
597      model/src: modifying do_oceanic_phys.F accordingly.
598    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
599    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
600      special setup of gmredi for which the adjoint is stable
601      enough for parameter optimization.
602    o bridging the gap between eddy stress and GM.
603      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
604          along with a change in CPP option (now ALLOW_EDDYPSI).
605      -> when using GM w/ GM_AdvForm:
606          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
607          is applied either in the tracer Eq. or in momentum Eq.
608          depending on data.gmredi (intro. GM_InMomAsStress).
609      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
610      The key modifications are in model/src/taueddy_external_forcing.F
611      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
612    
613    checkpoint59r
614    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
615      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
616      fix option to read coriolis(@ cell-corner) from files with CS-grid.
617    o pkg/mnc: add some attributes to standard 1D-coordinate variables
618    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
619      mass points, when using mnc for output
620      - add runtime parameter (missing_value, missing_value_int) to override
621        default (which is the value of getcon('UNDEF'))
622    o pkg/mnc: prepare mnc for the actual use of missing values with the
623      diagnostics package: small fix in mnc_cw_readwrite.template and more
624      initialisation of never used fields
625      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
626      versions
627    o pkg/thsice/thsice_ini_vars.F added default initial values so that
628      thermodynamics sea ice solver does not blow up when some initial fields
629      are missing.
630    o move from external_forcing_surf.F to ini_forcing.F
631      the p-coord. hack consisting in using pLoad to set phi0surf ;
632      update output of tutorial_global_oce_in_p (affected @ truncation level).
633    o Freshen up a bit hs94.1x64x5, notably:
634      remove rotationPeriod and tRef=5*0. (adjoint only), and add
635      exactConserv=.TRUE.
636    o pkg/generic_advdiff:
637      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
638      applies to files where Temperature & Salinity 2nd Order moments are used.
639    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
640      this uses a dynamically allocated internal state data structure
641      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
642      and requires a fortran 90 compiler
643    
644    checkpoint59q
645    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
646       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
647    o Refresh tutorial_global_oce_biogeo, notably:
648      - change bathymetry (put back seamounts in ACC, use hFacs)
649      - change EOS (POLY3 --> JMD95Z)
650      - use Bryan-Lewis vertical diffusivity
651      - use multidimensional advection
652      - remove old virtual virtual in dic pkg, now done through ptracer pkg
653      - change a couple of parameters in dic pkg
654    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
655    o pkg/obcs: change default to OBCSfixTopo = .true.,
656      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
657      - replace "debugMode" with "debugLevel .GE. debLevB"
658    o implementation of TAF directives for gchem,cfc,dic
659    o remove "exp5" (replaced by tutorial_deep_convection).
660    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
661      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
662      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
663      --> changes results in exp4, seaice_obcs
664    o tutorial_deep_convection :
665      update the set-up and increase resolution and domain size ; start
666      from pseudo initial conditions = output at t=120mn in order to see
667      something happening when running testreport.
668    o pkg/seaice: add os7mp as an advection scheme
669                  add check for advection schemes
670                  add a flag for restoring T and S underneath sea ice
671    o pkg/my82: add netcdf-support and diagnostics
672    o thsice pkg:
673      - Now hsMax limits snow height by turning it into ice following
674        flooding scheme (and now conserving energy)
675      - Slight rewriting of the formula in thsice_calc_thick.F
676      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
677      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
678    
679    checkpoint59p
680    o gchem / dic / cfc :
681      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
682      - add new parameter files: "data.dic" & "data.cfc" ;
683      - various re-arrangement in initialisation & header file ;
684      - fix tutorial_global_oce_biogeo for multi-threaded test.
685    o pkg/dic: test for "pickup_dic" file when restarting ;
686      if no pickup-file, can restart with a re-initialised pH (same as it did
687      before) providing pickupStrictlyMatch is set to False.
688    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
689      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
690    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
691      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
692    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
693     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
694       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
695    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
696       scheme to use for vorticty-term ;
697     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
698       (with default selectVortScheme, return to original discretisation)
699     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
700    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
701    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
702      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
703      also fix diagnostics VISCAHW & VISCA4W.
704    
705    checkpoint59o
706    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
707    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
708      move a few statemens out the main loop into separate loops
709    o pkg/shelfice:
710      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
711        (kg/m^2/s), does not break tests, because in verification/isomip,
712        rhoConstFresh=rhoConst (by accident)
713      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
714      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
715        new file model/src/seawater.F, so that they are available for all pkgs.
716      - convert potential temperature into in-situ temperature. This changes the
717        isomip tests => update tests
718    o add a flag writePickupAtEnd (default=true) to be able to suppress
719      writing a pickup at the last timestep
720    o tools/mpack-1.6 :
721      - disable automake (not working) and autoconf (not needed).
722      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
723        also cleaner with much less compilation warnings.
724    o pkg/profiles:
725      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
726      (for "less than 32 characters name" compiler requirement)
727    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
728      conditions that have a different sampling frequency than S/T/U/V obcs
729    o pkg/diagnostics (stats-diags):
730      - fix global Min/Max in case 1 processor get only empty tiles
731    o genmake2: replace (4 times)
732         make genmake_tc_1.o >> genmake_warnings 2>&1
733      with
734         COMM="$CC $CFLAGS -c genmake_tc_1.c"
735         echo $COMM >> genmake_warnings
736         $COMM >> genmake_warnings 2>&1
737      to make genmake2 always see the value of CC as specified in the optfile.
738    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
739      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
740      - modify verification advect_cs test to test SOM-advection on CS-grid.
741    o pkg/ctrl:
742      - Rewrite of ctrl_map_ini_ecco.F,
743        introducing a generic routine (ctrl_map_ini_gen.F).
744      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
745    
746    checkpoint59n
747    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
748      number in dedicate array "hdiag":
749      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
750        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
751      - many small changes (integer format) for large number of diagnostics
752      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
753        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
754    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
755      usingSphericalGrid, this allows to define the rotated grid coordinates
756      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
757      geographical coordinates according to the inverse of the rotation defined
758      by the Euler angles, so that Coriolis parameter and online-interpolation by
759      exf works with the geographical coordinates on XC/YC/XG/YG.
760      Naturally, this feature does not work with all packages, so some
761      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
762      profiles), because there the coordinates are assumed to be regular
763      spherical grid coordinates.
764    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
765      - introduce isopycnal diffusion coefficient control.
766    o tools/adjoint_options:
767      - additional control vector components.
768    o pkg/mnc: have mnc create marginally meaning full coordinate variables
769      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
770    o pkg/mypackage:
771      - add example of read/write pickup for state-var ;
772      - add entry points to the main code for state-vars diags & write-pickup.
773    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
774      transitions for useExfYearlyFields
775      - add new subroutine that determines the file to read from for
776        use*YearlyFields = .TRUE. and .FALSE.
777      - add a verification experiment to global_with_exf that tests
778        useExfYearlyFields with USE_EXF_INTERPOLATION defined
779    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
780      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
781      subroutines (which could be generated from a template, because they are
782      almost identical), for now they are included in obcs_prescribe_read.F for
783      simplicity
784    o pkg/exf:
785      - add a little more diagnostic to exf_interp_read (in analogy to
786        mds_read_field, can be turned off with debugLevel < debugLevA=1)
787      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
788        ugly but fast by unrolling short inner loops, inserting a unroll=8
789        directive in routine lagran, and splitting a loop and making do while the
790        outermost loop (the latter requires the intoduction of index arrays)
791    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
792    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
793      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
794    o verification/seaice_obcs: updated for restart test and latest options
795    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
796      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
797      for now this is only available for the C-grid code and also within
798      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
799    
800    checkpoint59m
801    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
802      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
803    o gad_som : fix flux output (& diagnostics) to have same units as other  
804      advection scheme fluxes (was previously multiplied by deltaT).  
805    o added verification/seaice_obcs both to test seaice open boundaries
806      and to provide an example matlab scrpt for generating them
807    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
808    o pkg/salt_plume: clean up salt_plume_frac.F to
809      remove redundancy in PlumeMethod 1 and 4
810    o pkg/kpp: added saltplume diagnostics
811    o pkg/obcs and pkg/seaice:
812      - do not set uice and vice to zero when OB*icefile are unspecified
813      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
814      - moved seaice tracer obcs after call to seaice_growth
815    o pkg/salt_plume: added various options for salt plume depth
816      criterion and for vertical distribution of the salt
817    
818    checkpoint59l
819    o pkg/ptracers: new version of ptracers pickup:
820      read meta file and write only fields which are needed to restart.
821      ( same logic as main pickup file ; also using pickupStrictlyMatch )
822    o pkg/seaice:
823      - add timescale for melting due to warm mixed layer as a means of
824        setting SEAICE_availHeatFrac more conveniently
825      - add a CPP-flag/runtime parameter check for flooding algorithm
826      - reformulated availHeat in seaice_growth.F to be independent of AREA
827    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
828      unit changes
829    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
830    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
831      SX vector computer.
832    o pkg/seaice:
833      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
834        seaice forcing fields can now be read only through pkg/exf
835      - removed some unused halos
836    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
837    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
838      or U/VICE from U/VWIND before computing U/VSTRESS
839    
840    checkpoint59k
841    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
842      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
843    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
844      all experiments pass when compile with un-initialised var. checking option.
845    o added pkg/salt_plume
846    o script to test restart (for now, in MITgcm_contrib/jmc_script)
847    o pkg/seaice: new read/write pickup version.
848      read meta file and write only fields which are needed to restart.
849      ( same logic as main pickup file ; also using pickupStrictlyMatch )
850    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
851    o lab_sea.hb87: modify the domain & update output.hb87.txt :
852      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
853      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
854      process. Fixed here by closing the domain at the Northern boundary.
855    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
856    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
857      a set of consecutive levels in/from a 3-D array.
858    o pkg/ptracers:
859      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
860      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
861    
862    checkpoint59j
863    o in pkgs: dic, obcs, offline, rbcs:
864      standard way to compute coeff. for time interpolation between 2 time reccords
865      which retains full precision (& make results less dependent on compiler).
866      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
867    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
868      packages instead of reading ice cover and wind speed separately
869    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
870     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
871      to allow to compile customized code before the update)
872    o cleaning-up:
873      - fix CPP instruction syntax in pkg/obcs
874      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
875        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
876      - fix some threads issue in IO parts.
877    o pkg/dic:
878      - add tons of "_d 0" (--> much better testreports !)
879       and then update outputs of tutorial_global_oce_biogeo
880    o pkg/mom_fluxform:
881      add a special version of momentum advection intended to conserve momentum
882      next to a bathymetry step or a coastline edge. (default = off = #undef)
883    o new read/write pickup version:
884      - for now, only implemented for main (mdsio) pickup file.
885      - write out only what is needed to restart; merge pickup_nh , pickup_ph
886        and main pickup together.
887      - read meta file; read only what is needed to restart; stop if a field
888        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
889        if it make sense (even if the restart is not perfect).
890      - if no meta file, assume that pickup to read corresponds exactly to
891        a pickup that would currently be written.
892      - read pickup written in the old format (until checkpoint59i) if it
893        recognizes an old meta file (no field-list).
894      - add a meta file in exp. which starts from a pickup: 2 cases:
895        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
896         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
897        b) a meta file describing the content of the associated pickup file
898         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
899    o pkg/mdsio & pkg/rw:
900      - new routine to read a meta file ; new set of routine to read
901        Multiple-fields file (with meta file).
902    o added open boundary conditions capability for seaice
903        HSNOW, HSALT, UICE, and VICE
904    
905    checkpoint59i
906    o adjoint:
907      * fix multiDimAdvection adjoint
908        (partial recomputation problem by TAF for fVerT(:,:,kDown)
909        and comlev1 size definition (maxpass vs. max. number of tracers)
910      * verification/global_ocean.90x45x15 adjoint now tests
911        NLFS and multiDimAdvection using DST3 (=30)
912      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
913    o pkg/kpp: add "_d 0" to real constant (if missing);
914      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
915      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
916    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
917      for internal parameters related to restart process (formerly from PARAMS.h)
918      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
919    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
920      as argument. (only atm2d & obcs write_pickup have not yet been updated)
921    o pkg/monitor:
922      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
923      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
924      - account for deep Atmosphere factor and density factor (anelastic)
925    o added open boundary conditions capability for seaice HEFF and AREA
926    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
927      thermodynamics
928      - requires a little reorganization, which affects the testreport results
929        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
930        so that now the conservative form is tested
931      - add a few comments
932    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
933    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
934    o add new diagnostics to seaice: advective, diffusive fluxes (only for
935      multidim-advection, for scheme 2 they are not filled) and transports,
936      thermodynamic growth rates
937    o change units of EmPmR (inside the code, + within coupling interface)
938      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
939      Affects results @ truncation level (cg2d match) and update output of
940       experiments: lab_sea(6), global_ocean.90x40x15(10),
941      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
942      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
943      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
944      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
945    
946    checkpoint59h
947    o pkg/exf:
948      - improve vectorization by moving if-statement out of loops in
949        exf_mapfields, exf_radiation
950      - exf_bulkformulae.F: introduce 2D fields and vectorize code
951    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
952    o testreport:
953      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
954        monitor & update offline_exf_seaice exp. output.
955      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
956    o pkg/seaice:
957      - bug fix in the evp solver: boundary conditions were affected be
958        masking of zMax/zMin (changes results)
959      - minor bug fix in boundary conditions in seaice_calc_strainrates
960        (changes results for no_slip)
961      - seaice_lsr.F: make interpolation of eta dependent on boundaries
962      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
963      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
964        stress formulation and no-slip boundary conditions
965    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
966      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
967    o pkg/seaice: a first HSALT time stepping equation has been checked in
968    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
969      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
970      without requiring DO-IF statements
971    o pkg/thsice:
972      use continuous power-law function for partition of energy between lateral
973      melting/freezing and thinning/thickening ; old code using step function
974      still available with #undef THSICE_FRACEN_POWERLAW
975      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
976    o testreport: change AD testing : check against results/output_adm.txt
977      using same scripts as for forward test.
978    
979    checkpoint59g
980    o adjoint testing: in preparation for changing testreport:
981      - output format: cost and grad written on separated lines
982      - ad output results in directory "results" (instead of "results_ad")
983    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
984    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
985    o pkg/ecco: allow user defined cost function contributions
986    o testreport:
987      Allow to choose (per experiment) the list of tested output variables
988       and the main variable (used to issue a pass/FAIL ) ;
989      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
990      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
991      Also modify printing of summary:
992       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
993       b) echo the list of tested variables in the individual summary.txt of
994          each experiment.
995    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
996      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
997      (but still depend on the tile decompostion of the domain).
998    o pkg/seaice: change a discretization detail to make the B-grid code
999      "more symmetric". This change is likely to remove all "ridges/leads" that
1000      where quasi-aligned with the grid in B-grid solutions. It may also be
1001      the solution to the stress coupling issues with the B-grid.
1002    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
1003      remove .cvsignore from input dir. (since testreport no longer run here).
1004    o pkg/thsice:
1005     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
1006     - fix reshaping of sea-ice just after advection:
1007       melt all the ice only if ice-volume is too small.
1008     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
1009       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
1010     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
1011    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
1012      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
1013    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
1014      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
1015      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
1016      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
1017      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
1018      -> update output.txt
1019    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
1020     this affects truncation error: -> update output.txt of exp:
1021      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
1022      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
1023    
1024    checkpoint59f
1025    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
1026    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
1027      a bounded range (in forward mode)
1028    o pkg/ecco, ctrl, autodiff and mom_common:
1029     internal parameter controls, completements of implementations
1030    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
1031    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
1032      (not seem any difference in testing results).
1033    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
1034       at face corners.
1035    o pkg/generic_advdiff:
1036     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
1037      loop range indices for computing vertical advection tendency
1038      and do the calculation in the interior only (no overlap) ;
1039      for now, only implemented for SOM advection (to save CPU time).
1040     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
1041    o exch2 adjoint
1042      First set of changes:
1043      - add exch2 hand-written adjoint templates
1044      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
1045        This will require cleanup in pkg/autodiff/*.F
1046        (changed routines currently kept separate in verif. code/)
1047      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
1048        that used to hide exch2 or cubed-sphere specific code
1049        (commented via 'cph-exch2')
1050    o pkg/seaice
1051      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
1052    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
1053       output of global_ocean.cs32x15.thsice .
1054    
1055    checkpoint59e
1056    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
1057      for B-grid vector (not yet tested) and C-grid vector (<- only used
1058      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
1059    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
1060      (#ifdef ALLOW_SALT_PLUME)
1061    o gather_2d/scatter_2d: removed halo regions
1062    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
1063      scheme and the corresponding test case (under front_relax dir). For now,
1064      only available with Skew-flux form and not yet tested in realistic set-up.
1065      adjoint: store directives updated, but gradient checks deteriorated,
1066      so maybe GM/Redi adjoint is now broken.
1067    o seaice adjoint
1068      * add AREA, HEFF, HSNOW as control variable
1069        (should not change lab_sea results)
1070      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
1071    o pkg/seaice:
1072      * added computation of saltFlux in seaice_growth;
1073        For time being, sea ice salinity is assumed constant
1074        contribution of snow flooding to freshening of sea ice is neglected.
1075        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
1076        defaults to 0.0 in order to maintain backward compatibility.
1077        Typical values for SEAICE_salinity are 4 to 10 g/kg.
1078      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
1079      * added SEAICE_availHeatFrac, which specifies fraction of surface level
1080        heat content used to melt or grow ice
1081      * commented out cap of HICE: it helps keep ice thinner
1082      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
1083      * applied OBCS T/S mask to HEFFM sea ice mask
1084    
1085    checkpoint59d
1086    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
1087     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
1088     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
1089    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
1090     and change default value of parameter "GM_Small_Number";
1091     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
1092       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
1093       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
1094    o pkg/ecco: cost function when applying pkg/smooth to controls
1095    o pkg/ctrl: add forcingPrecond run time parameter
1096    o pkg/seaice:
1097     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
1098     - fix bug in metric terms of u-equation in LSR solver (implicit part),
1099       changes verification/lab_sea
1100     - rearrange implicit part of u-equation in LSR solver to make it easier to
1101       read, understand, and debug. This causes changes at the truncation level.
1102     - fix (serious) bug in the boundary conditions (sign error in the implicit
1103       part) of the LSR solver. Changes all LSR results.
1104     - fixed problem with HSNOW initialization to avoid thick snow when AREA
1105       is initilized with small values - does not change lab_sea results.
1106     - added HsnowFile initialization capability
1107    o pkg/smooth: addition to model/src and pkg/ctrl so allow
1108     initialization of pkg/smooth and application to control vector
1109    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
1110    o dependencies: pkg/profiles requires pkg/cal
1111    o pkg/profiles:
1112     - added option ALLOW_PROFILES_GENERICGRID
1113         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
1114         that interpolation information (grid points and coefficients) is provided
1115         within the netcdf input files.
1116         -> sample matlab scripts can be found in MITgcm_contrib/gael
1117         that allow you to prepare netcdf input files.
1118     - also modified: cleaner include statements, cleaner error print statements,
1119       cleaner stops when error, and more tests of the netcdf input files consistency.
1120    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
1121    o pkg/seaice:
1122     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
1123       requires a new routine: seaice_diagnostics_fill.F
1124     - make sure that seaice does not move if not forced (pressure replacement
1125       method, Hibler and Ip, 1995), changes results
1126     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
1127     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
1128       It is turned off by default (=-1.), because it changes the results.
1129     - make it possible to read AREA from a file, too.
1130    
1131    checkpoint59c
1132    o add S/R and diagnostics for oceanic mixed-layer depth
1133    o move GMRedi call after all vertical mixing schemes (including KPP)
1134    o pkg/thsice:
1135     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
1136      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
1137  o pkg/obcs:  o pkg/obcs:
1138   - bug fix for balance code   - bug fix for balance code
1139  o pkg/seaice:  o pkg/seaice:
# Line 18  o change calculation of Visbeck K: Line 1148  o change calculation of Visbeck K:
1148    - no longer depend on tapering scheme; instead, compute slope (limited    - no longer depend on tapering scheme; instead, compute slope (limited
1149      by GM_maxSlope). this is equivalent to what was comuted before with      by GM_maxSlope). this is equivalent to what was comuted before with
1150      clipping or linear tappering.      clipping or linear tappering.
1151    - fix vertical averaging (wrong by 1 level)    - fix vertical averaging (wrong by 1/2 level)
1152    - leave the old version (but will not be maintained) within    - leave the old version (but will not be maintained) within
1153      #ifdef OLD_VISBECK_CALC / #endif      #ifdef OLD_VISBECK_CALC / #endif
1154      - update output of exp. ideal_2D_oce
1155  o change error catch in calc_r_star to improve vectorization  o change error catch in calc_r_star to improve vectorization
1156  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
1157    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
1158    o adjoint:
1159      Re-organized adjoint checkpointing according to Matt Mazloff
1160      (but with modifs/completions/cleanups)
1161      Storing is now bundled into large arrays to optimized I/O
1162      (and second step in cleanup of the_main_loop)
1163    
1164  checkpoint59b  checkpoint59b
1165  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 77  o pkg/exf: some cleaning-up: Line 1213  o pkg/exf: some cleaning-up:
1213  o pkg/thsice:  o pkg/thsice:
1214   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
1215    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
1216    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
1217    and in thsice_extend.F:    and in thsice_extend.F:
1218    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
1219    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 114  o in FFIELDS.h: Line 1250  o in FFIELDS.h:
1250       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
1251  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
1252  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
1253      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
1254        are no longer updating the vertical diffusivity array
1255        (passed as argument) but are (re-) setting those arrays.
1256  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
1257    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
1258      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 1596  o add two new packages Line 2734  o add two new packages
2734    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2735    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2736      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2737      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2738  o add offline package  o add offline package
2739  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2740    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
Legend:
Removed from v.1.826  
changed lines
  Added in v.1.1159
  ViewVC Help
Powered by ViewVC 1.1.22