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revision 1.957 by mlosch, Wed Feb 13 07:43:39 2008 UTC revision 1.1128 by mlosch, Mon Jun 22 15:33:02 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61q
8    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
9     - the boundary conditions along open boundaries are unclear, because the
10       associated masks are set to zero and are thus treated as closed when
11       applying the slip-boundary conditions.
12     - move initialisation of grid variables from seaice_init_varia to _fixed
13    o adding doc/diags_changes.txt
14    o model/src:
15      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
16       to avoid "_diags" naming if no relation to pkg/diagnostics.
17      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
18       file and only call PLOT_FIELD_XYZ if debugMode=T.
19      remove few PLOT_FIELD_XY calls outside initialisation.
20      remove few unnecessary BARRIER.
21    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
22      of salt_plume package in Southern Ocean
23    o pkg/thsice:
24     - fix hOceMxL in overlap (needed for sea-ice advection);
25       update output of experiment global_ocean.cs32x15.icedyn.
26    o pkg/seaice:
27     - make the (placeholder-)tracer IceAge a little more meaningful
28      by avoiding ridging of age due to convergent ice flow
29     - add diagnostics for surface temperature, atmospheric and oceanic
30       heat flux, and atmospheric and oceanic ice growth
31    
32    checkpoint61p
33    o eesupp (global_max & global_sum):
34     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
35     - remove starting & endding barrier (no longer needed)
36    o pkg/mdsio, writelocal:
37       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
38       (remove the STOP): uses shared buffer IO to store data from all threads
39       and then let master-thread write nThreads tiles.
40    o pkg/mdsio (read/write field):
41     - tiled IO done in 1 piece (all levels at a time);
42     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
43     - multi-threaded: allow to read/write local (non-shared) array
44       (was already working with singleCpuIO ; now works also without);
45       => no longer needs barrier call after reading a file (added inside
46       mds_read/write field).
47     - move barrier calls outside gather/scatter_2d to mds_read/write_field
48    o pkg/obcs/exf
49      - exf_getffieldrec.F: add a few ". _d 0" and
50                            add code to catch the case fldperiod = 0.  
51      - obcs_precribe_read.F: change if statements so that they match
52                              the variable type (_RL)
53      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
54        exf_iprec) as part of namelist EXF_NML_01
55    o pkg/mdsio:
56      - read/write tiled (local) files: read/write 1-level tile chunk at a time
57        (instead of segment of length sNx); expected to speed up tiled IO.
58    o pkg/exch2:
59      - take buffer copy from/to array out of S/R exch2_send/recv into new
60        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
61        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
62      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
63      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
64        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
65        including Topology header file (and common blocks).
66      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
67        remove 2nd exch call in exch2_s3d_rx (no longer needed).
68      - document S/R arg. list (+ update some comments)
69    o pkg/seaice:
70      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
71        temperature and humidity over sea ice based on climatological values.
72      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
73        of LSR (this change is expected to change the results slightly because now
74        it uses slightly difference moduli from the second last LSR solution, but
75        that is more consistent with the stress computations; this part of the code
76        is not tested in the verification experiments)
77      - fix diagnostics for flux of ice in case of B-grid
78      - turn strain rates eij and press into global fields within global
79        common block in SEAICE.h for more straighforward diagnostics
80      - fix diagnostics for principal stress components, press, zeta, eta
81        to give something meaning full
82    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
83      new output (all 4 tests) using default rotationPeriod.
84    o pkg KPP:
85      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
86      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
87        and normal grid from 1 to Nr)
88    o Fix computations of L4rdt in mom_calc_visc.F
89    o eesupp:
90      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
91      should be called before a "stop" if we know that all process are going
92      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
93    
94    checkpoint61o
95    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
96    o model/src/ini_curvilinear_grid.F:
97       compute angleSin/CosC when they are not read from a file
98    o pkg/seaice:
99       add pseudo time stepping for LSOR
100    o pkg/exch2:
101       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
102    o pkg/seaice:
103       Adding separate sea ice albedo, drag coefficients, and HO in Southern
104       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
105    o SingleCpuIO:
106       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
107    o pkg/seaice:
108       put exchanged variable in (local) common block for MPI+Multi-Threads
109       to work (necessary with exch1, and for now with exch2 too).
110    o verification: to get more experiments tested with mpi, mth and mpi+mth,
111      change tiling of:
112       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
113       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
114      update output of exp:
115       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
116       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
117      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
118                       (note: output.txt generated on faulks using only 1 tile)
119    o eesupp & mdsio (SingleCpuIO):
120     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
121       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
122       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
123     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
124     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
125       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
126    o pkg/exch2:
127     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
128       read parameter file "data.exch2" if it exists; otherwise try default regular
129       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
130     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
131       with new code (not to be used, just as a backup solution).
132     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
133       in utils/exch2/input.
134    
135    checkpoint61n
136    o eesupp & mdsio (SingleCpuIO):
137      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
138        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
139        receive real*4 array (instead of real*8) to read/write 32.bit files.
140        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
141         and remove new mapping S/R)
142    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
143      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
144        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
145        when using exch2. Add S/R to map global io-buffer to global model array.
146      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
147    
148    checkpoint61m
149    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
150      and add 3 other S/R for other types (R4,R8,RS).
151      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
152    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
153     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
154     - reduce number of macro definitions (keep only those which are used);
155       can always call directly the corrresponding S/R if needed.
156     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
157       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
158     Fixed wrong type of arg in:
159       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
160       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
161     To fix: global_sum of var in common block is wrong (multi-threaded) in:
162       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
163     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
164    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
165      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
166    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
167    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
168      edges are closed (zero depth); might happen with "blank tiles";
169      for now, disabled if using OBCS.
170    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
171      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
172    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
173      to reduce length of 1.D array print in STDOUT.
174    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
175      + use 48 tiles (16x8): this will allow to test "blank tiles".
176    o start to test MPI + multi-threaded (change testreport to skip tests
177      where number of tiles do not match).
178    o genmake2: add option "-omp" to turn on Open-MP ;
179      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
180    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
181      and keep the original tile numbering. Note: compatible with old
182      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
183    
184    checkpoint61l
185    o Overlaps had been forgotten in calculating ijk keys : fixed
186    o fix cyrus makedepend for gcc 4.4
187    o experiment fizhi-cs-aqualev20:
188      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
189      and generate new output. Note: new output is much closer to the old
190      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
191      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
192    o pkg/fizhi:
193     - change to avoid indices going deliberately over array-bounds
194     - remove unnecessary MPI stuff
195     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
196     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
197       does not go over array-bounds and therefore returns reliable output.
198     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
199       this S/R has 4 output arguments, which are used inside "get_alarm";
200       when it is called with the same variable "ndum" in place of several
201       output arguments, this produces weird side effect inside "get_alarm"
202      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
203       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
204       address) and produces error.
205    o tools/gemake2: (March 27-29 2009)
206      with option "-mpi": link *_mpi files from "MODS" dir (this is what
207      testreport does).
208    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
209    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
210       update lab_sea.lsr & lab_sea.salt_plume results
211    o pkg/seaice:
212      Major overhaul of the LSOR solver: change discretization from original
213      finite differences to finite volume. The old routine is still in the
214      file seaice_lsr.F and can be turned on with the CPP-flag
215      SEAICE_OLD_AND_BAD_DISCRETIZATION
216      Along with this change, the discretization of the strain rates is changed.
217      The same flag turns on the old discretization in seaice_calc_strainrates.F
218      All verification experiments with seaice are affected (except for
219      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
220      results by setting the above flag.
221      Further changes involve changes in defaults:
222      - ALLOW_FLOODING is defined and turned on by default
223      - SEAICEadvSnow = .true. is now the default
224      - SEAICEadvSalt = .true. is now the default
225      - SEAICEadvAge  = .true. is now the default
226      - SEAICE_clipVelocities  = .false. is now the default
227                                         (as per J. Zhang's recommendation)
228      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
229        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
230      - seaice_growth: replace computation of UG by a simple copy from wspeed
231    
232    checkpoint61k
233    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
234      seaice_lsr: fixed a few metric terms,
235                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
236                  add more debugging diagnostics
237      seaice_evp: removed superfluous many metric terms of FV discretization
238                  of stress divergence
239                  affects lab_sea, lab_sea.hb87
240      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
241                  of stress divergence for non-evp solver
242                  (this part is not tested anywhere)
243      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
244                  they were effectively only half slip
245                  affects lab_sea.hb87
246      updated all relevant verification experiments (except lab_sea//output_adm.txt
247        which was left over, but fails at level 7 & 6)
248    
249    checkpoint61j
250    o pkg/seaice: turn a few hard wired parameters into run time parameters
251    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
252      time in seconds as promised by the usints in seaice_monitor and exf_monitor
253    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
254      that are not cubed-sphere grids
255    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
256    o pkg/ctrl:
257      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
258    o non-hydrostatic (calc_gw.F):
259      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
260      update output of exp. global_ocean.cs32x15.viscA4
261    o remove backward compatibility for thetaMin,phiMin
262      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
263    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
264      interpolated wind field not only for curvilineargrid=.true., but also
265      for a rotated grid (rotateGrid=.true.)
266    o pkg/exf: add capability to bypass interpolation for runoff
267      by setting yet another CPP-flag
268    o eesupp/src, B-grid exchange:
269      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
270    o autodiff
271      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
272      allows to switch to single-prec common blocks;
273      corresponding switch occurs in tamc.h, integer isbyte
274      TAF store directivs "byte" and "kind" seem equivalent;
275      Most tamc.h have been updated correspondingly.
276    
277    checkpoint61i
278    o autodiff:
279      fix autodiff_sore/_restore indices for obcs
280      (spotted by I. Hoteit, M. Mazloff)
281    o pkg/autodiff, pkg/ctrl:
282      Add flag to reduce all tapelev I/O to single-prec.
283      In data.ctrl set
284        doSinglePrecTapelev = .TRUE.
285    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
286      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
287    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
288      real fresh water flux (not yet)
289    o pkg/mdsio & rw:
290     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
291     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
292    o pkg/flt:
293     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
294       init_fixed & ini_varia.
295     - clean-up & simplify linear interpolation S/R:
296       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
297     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
298     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
299     - add vert. coordinate & horiz. indices to output files.
300     - change vertical position in initial condition, from index to depth [m].
301     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
302       (easier to get to a curvilinear grid) ; delX,delY no longer used.
303    o pkg/ggl90: a few modifications:
304     - fix bottom boundary condition, and interpolation of KappaE
305       near top and bottom
306     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
307     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
308     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
309    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
310      (maintain temporary backward compatibility, until next checkpoint)
311    
312    checkpoint61h
313    o pkg/diagnostics with "periodic averaging diagnostics":
314      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
315    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
316    o pkg/obcs: fix loop ranges for balancing code
317    o pkg/flt:
318     - improve criteria for finding which tile owns a float.
319     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
320    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
321      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
322      with ocean biogeo)
323    o pkg/flt:
324     - do some cleaning and fix the restart ;
325     - add output.txt in flt_example/results to get this pkg tested.
326    o genmake2: add an EXTENDED_SRC option and flag.
327       for now, cannot be turned on on command line (only through genmake_local)
328    o pkg/mdsio: read/write vector:
329     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
330     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
331       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
332     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
333      (drop to 4 digits matching for grad). But this test does not look very
334      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
335    
336    checkpoint61g
337    o pkg/flt:
338      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
339       + make OPTIONS file more standard.
340      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
341      - fix _BYTESWAPIO CPP-Flag
342      - standard reading of file-parameter "data.flt"
343      - fix argument list of S/R FLT_RESTART
344      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
345    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
346    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
347      a still unfixed compiler/optimization bug
348    
349    checkpoint61f
350    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
351      update results of global_ocean.cs32x15.icedyn test.
352    o move getcon.F from model/src to pkg/fizhi.
353    o pkg/exf: add parameter for extrapolation of temp up to the surface
354       and option to prevent negative evap (in bulk_largeyeager04 only).
355    o Prather Advection scheme: fix tracer conservation for divergent flow
356      (e.g., when using NonLin Free-Surface).
357    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
358    o gmredi (Visbeck-variable-K):
359     - add more parameters to Visbeck-variable-K.
360     - use a 5 points average for dSigmaR in Visbeck-K calculation
361       (more "homogenous": same stencil and same weights as in dSigmaH)
362     - update output of ideal_2D_oce experiment.
363    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
364      (#undef REAL4_IS_SLOW)
365     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
366       coordinate variable
367     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
368       (surface forcing fields), removes some of the functionality
369     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
370     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
371       probably not all: copy _RS surface flux fields to RL field before
372       calling DIAGNOSTICS_FILL
373     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
374       real*4 (CALL EXCH_*_RS) versions.
375     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
376       (generate new output).
377    
378    checkpoint61e
379    o gmredi (Visbeck-variable-K):
380      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
381      - change computation of Visbeck-K where Slope > Smax :        
382        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
383        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
384    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
385      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
386    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
387    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
388      does not become too large (to avoid precision problems in implicit-diffusion
389      solver); update ideal_2D_oce output.
390    o pkg ggl90:
391      - in ggl90_cal.F: compute only one set of visc/diff, used to
392        step forward TKE/T/S/momentum
393      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
394        have Prandlt =1)
395    o gmredi (fm07):
396      - add lower limit on Transition layer thickness + lower limit on 1/lambda
397      - allow to set few more params from data.gmredi
398    o pkg ggl90:
399          - add missing sqrt(2) factor in computation of mixing length
400            scale in ggl90_calc.F
401            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
402    
403    checkpoint61d
404    o adjoint modifs
405      - adapt to new field rhoInSitu
406      - allow to revert from StoreDynVars2D, StoreDynVars3D
407        to individual fields
408        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
409    o store 3-D (in-situ) density in commom block (DYNVARS.h)
410     - save 1 rho computation.
411     - no longer modify T & S inland when using down_slope pkg.
412    o gad_som : allow to switch to SOM advection for T & S without corresponding
413      pickup files (using new S/R: MDS_CHECK4FILE).
414    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
415      (for useSingleCpuIO to work in multi-threaded)
416    o pkg/shelfice:
417     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
418       with SHELFICEtopoFile in data.shelfice
419     - move code for reading ice shelf topography and modifying hFacC into separate
420       subroutines of the shelfice package
421     - separate initialisation of "fixed" and "variable" variables
422     - kTopC is not (yet) replaced by kSurfC, although this is possible
423    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
424    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
425      and rename:
426      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
427      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
428    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
429    
430    checkpoint61c
431    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
432      to add mass source/sink of fluid in the interior (3-D generalisation
433      of oceanic real-fresh water flux).
434    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
435    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
436    o new pkg: down_slope
437      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
438      - presently, modify T & S inland (dwnslp_calc_rho.F).
439        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
440      - implementation for ocean in P-coords not tested.
441      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
442    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
443      (to facilitate conversion of oceanic pkg to p-coordinate).
444    o change FIND_RHO to FIND_RHO_2D :
445      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
446    o new pkg: cheapaml
447    
448    checkpoint61b
449    o exch2:
450      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
451      - no longer depend on the order sequence (N,S,E,W).
452      - 3rd exchange no longer needed (tested with 24 tiles).
453      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
454      - exch_UV_A-grid readily available (but not yet tested).
455      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
456      (both are no longer needed) in exch_uv: no effect in forward run; but
457       get truncation error differences with adjoint exch.
458    o exch2:
459     - change index-bounds storage (moved from target to local tile,
460       more intuitive this way) ; rename/remove some variables.
461     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
462    
463    checkpoint61a
464    o exch2/matlab-topology-generator:
465      fix bug in index bounds for N-S internal exchange (hard to tell if this
466      had any effect on the solution).
467    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
468      is exceeded
469    o testreport: modify syntax of awk, so that it works also with
470      awk, and not only with nawk and gawk
471    
472    checkpoint61
473    o autodiff
474      Change default for TAF usage by removing argument '-nonew_arg'
475      This changes TAF subroutine argument list (ordering of active var.)
476      Omission of this flag leads to incompatibility w.r.t. TAMC
477      To restore TAMC-compatibility, need following modifs:
478      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
479      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
480      Tested TAF version is 1.9.22
481      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
482    
483    checkpoint60
484    --->>> This is the last checkpoint for which generating the adjoint
485    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
486    --->>> by default.
487    --->>> Future checkpoints will ommit this flag by default.
488    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
489    o pkg/grdchk: Add gradient check to etan0 perturbations.
490    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
491    o pkg/autodiff: more flexibility in zeroadj.
492      model/src: modifying do_oceanic_phys.F accordingly.
493    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
494    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
495      special setup of gmredi for which the adjoint is stable
496      enough for parameter optimization.
497    o bridging the gap between eddy stress and GM.
498      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
499          along with a change in CPP option (now ALLOW_EDDYPSI).
500      -> when using GM w/ GM_AdvForm:
501          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
502          is applied either in the tracer Eq. or in momentum Eq.
503          depending on data.gmredi (intro. GM_InMomAsStress).
504      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
505      The key modifications are in model/src/taueddy_external_forcing.F
506      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
507    
508    checkpoint59r
509    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
510      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
511      fix option to read coriolis(@ cell-corner) from files with CS-grid.
512    o pkg/mnc: add some attributes to standard 1D-coordinate variables
513    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
514      mass points, when using mnc for output
515      - add runtime parameter (missing_value, missing_value_int) to override
516        default (which is the value of getcon('UNDEF'))
517    o pkg/mnc: prepare mnc for the actual use of missing values with the
518      diagnostics package: small fix in mnc_cw_readwrite.template and more
519      initialisation of never used fields
520      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
521      versions
522    o pkg/thsice/thsice_ini_vars.F added default initial values so that
523      thermodynamics sea ice solver does not blow up when some initial fields
524      are missing.
525    o move from external_forcing_surf.F to ini_forcing.F
526      the p-coord. hack consisting in using pLoad to set phi0surf ;
527      update output of tutorial_global_oce_in_p (affected @ truncation level).
528    o Freshen up a bit hs94.1x64x5, notably:
529      remove rotationPeriod and tRef=5*0. (adjoint only), and add
530      exactConserv=.TRUE.
531    o pkg/generic_advdiff:
532      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
533      applies to files where Temperature & Salinity 2nd Order moments are used.
534    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
535      this uses a dynamically allocated internal state data structure
536      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
537      and requires a fortran 90 compiler
538    
539    checkpoint59q
540    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
541       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
542    o Refresh tutorial_global_oce_biogeo, notably:
543      - change bathymetry (put back seamounts in ACC, use hFacs)
544      - change EOS (POLY3 --> JMD95Z)
545      - use Bryan-Lewis vertical diffusivity
546      - use multidimensional advection
547      - remove old virtual virtual in dic pkg, now done through ptracer pkg
548      - change a couple of parameters in dic pkg
549    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
550    o pkg/obcs: change default to OBCSfixTopo = .true.,
551      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
552      - replace "debugMode" with "debugLevel .GE. debLevB"
553    o implementation of TAF directives for gchem,cfc,dic
554    o remove "exp5" (replaced by tutorial_deep_convection).
555    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
556      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
557      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
558      --> changes results in exp4, seaice_obcs
559    o tutorial_deep_convection :
560      update the set-up and increase resolution and domain size ; start
561      from pseudo initial conditions = output at t=120mn in order to see
562      something happening when running testreport.
563    o pkg/seaice: add os7mp as an advection scheme
564                  add check for advection schemes
565                  add a flag for restoring T and S underneath sea ice
566    o pkg/my82: add netcdf-support and diagnostics
567    o thsice pkg:
568      - Now hsMax limits snow height by turning it into ice following
569        flooding scheme (and now conserving energy)
570      - Slight rewriting of the formula in thsice_calc_thick.F
571      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
572      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
573    
574    checkpoint59p
575    o gchem / dic / cfc :
576      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
577      - add new parameter files: "data.dic" & "data.cfc" ;
578      - various re-arrangement in initialisation & header file ;
579      - fix tutorial_global_oce_biogeo for multi-threaded test.
580    o pkg/dic: test for "pickup_dic" file when restarting ;
581      if no pickup-file, can restart with a re-initialised pH (same as it did
582      before) providing pickupStrictlyMatch is set to False.
583    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
584      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
585    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
586      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
587    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
588     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
589       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
590    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
591       scheme to use for vorticty-term ;
592     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
593       (with default selectVortScheme, return to original discretisation)
594     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
595    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
596    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
597      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
598      also fix diagnostics VISCAHW & VISCA4W.
599    
600    checkpoint59o
601    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
602    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
603      move a few statemens out the main loop into separate loops
604    o pkg/shelfice:
605      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
606        (kg/m^2/s), does not break tests, because in verification/isomip,
607        rhoConstFresh=rhoConst (by accident)
608      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
609      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
610        new file model/src/seawater.F, so that they are available for all pkgs.
611      - convert potential temperature into in-situ temperature. This changes the
612        isomip tests => update tests
613    o add a flag writePickupAtEnd (default=true) to be able to suppress
614      writing a pickup at the last timestep
615    o tools/mpack-1.6 :
616      - disable automake (not working) and autoconf (not needed).
617      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
618        also cleaner with much less compilation warnings.
619    o pkg/profiles:
620      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
621      (for "less than 32 characters name" compiler requirement)
622    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
623      conditions that have a different sampling frequency than S/T/U/V obcs
624    o pkg/diagnostics (stats-diags):
625      - fix global Min/Max in case 1 processor get only empty tiles
626  o genmake2: replace (4 times)  o genmake2: replace (4 times)
627       make genmake_tc_1.o >> genmake_warnings 2>&1       make genmake_tc_1.o >> genmake_warnings 2>&1
628    with    with
# Line 2010  o add two new packages Line 2629  o add two new packages
2629    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2630    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2631      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2632      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2633  o add offline package  o add offline package
2634  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2635    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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