/[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 1.928 by jmc, Tue Dec 18 16:19:53 2007 UTC revision 1.1115 by mlosch, Tue Jun 2 15:01:00 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/obcs/exf
8      - obcs_precribe_read.F: change if statements so that they match
9                              the variable type (_RL)
10      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
11        exf_iprec) as part of namelist EXF_NML_01
12    o pkg/mdsio:
13      - read/write tiled (local) files: read/write 1-level tile chunk at a time
14        (instead of segment of length sNx); expected to speed up tiled IO.
15    o pkg/exch2:
16      - take buffer copy from/to array out of S/R exch2_send/recv into new
17        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
18        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
19      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
20      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
21        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
22        including Topology header file (and common blocks).
23      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
24        remove 2nd exch call in exch2_s3d_rx (no longer needed).
25      - document S/R arg. list (+ update some comments)
26    o pkg/seaice:
27      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
28        of LSR (this change is expected to change the results slightly because now
29        it uses slightly difference moduli from the second last LSR solution, but
30        that is more consistent with the stress computations; this part of the code
31        is not tested in the verification experiments)
32      - fix diagnostics for flux of ice in case of B-grid
33      - turn strain rates eij and press into global fields within global
34        common block in SEAICE.h for more straighforward diagnostics
35      - fix diagnostics for principal stress components, press, zeta, eta
36        to give something meaning full
37    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
38      new output (all 4 tests) using default rotationPeriod.
39    o pkg KPP:
40      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
41      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
42        and normal grid from 1 to Nr)
43    o Fix computations of L4rdt in mom_calc_visc.F
44    o eesupp:
45      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
46      should be called before a "stop" if we know that all process are going
47      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
48    
49    checkpoint61o
50    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
51    o model/src/ini_curvilinear_grid.F:
52       compute angleSin/CosC when they are not read from a file
53    o pkg/seaice:
54       add pseudo time stepping for LSOR
55    o pkg/exch2:
56       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
57    o pkg/seaice:
58       Adding separate sea ice albedo, drag coefficients, and HO in Southern
59       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
60    o SingleCpuIO:
61       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
62    o pkg/seaice:
63       put exchanged variable in (local) common block for MPI+Multi-Threads
64       to work (necessary with exch1, and for now with exch2 too).
65    o verification: to get more experiments tested with mpi, mth and mpi+mth,
66      change tiling of:
67       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
68       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
69      update output of exp:
70       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
71       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
72      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
73                       (note: output.txt generated on faulks using only 1 tile)
74    o eesupp & mdsio (SingleCpuIO):
75     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
76       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
77       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
78     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
79     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
80       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
81    o pkg/exch2:
82     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
83       read parameter file "data.exch2" if it exists; otherwise try default regular
84       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
85     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
86       with new code (not to be used, just as a backup solution).
87     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
88       in utils/exch2/input.
89    
90    checkpoint61n
91    o eesupp & mdsio (SingleCpuIO):
92      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
93        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
94        receive real*4 array (instead of real*8) to read/write 32.bit files.
95        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
96         and remove new mapping S/R)
97    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
98      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
99        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
100        when using exch2. Add S/R to map global io-buffer to global model array.
101      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
102    
103    checkpoint61m
104    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
105      and add 3 other S/R for other types (R4,R8,RS).
106      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
107    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
108     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
109     - reduce number of macro definitions (keep only those which are used);
110       can always call directly the corrresponding S/R if needed.
111     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
112       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
113     Fixed wrong type of arg in:
114       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
115       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
116     To fix: global_sum of var in common block is wrong (multi-threaded) in:
117       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
118     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
119    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
120      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
121    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
122    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
123      edges are closed (zero depth); might happen with "blank tiles";
124      for now, disabled if using OBCS.
125    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
126      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
127    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
128      to reduce length of 1.D array print in STDOUT.
129    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
130      + use 48 tiles (16x8): this will allow to test "blank tiles".
131    o start to test MPI + multi-threaded (change testreport to skip tests
132      where number of tiles do not match).
133    o genmake2: add option "-omp" to turn on Open-MP ;
134      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
135    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
136      and keep the original tile numbering. Note: compatible with old
137      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
138    
139    checkpoint61l
140    o Overlaps had been forgotten in calculating ijk keys : fixed
141    o fix cyrus makedepend for gcc 4.4
142    o experiment fizhi-cs-aqualev20:
143      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
144      and generate new output. Note: new output is much closer to the old
145      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
146      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
147    o pkg/fizhi:
148     - change to avoid indices going deliberately over array-bounds
149     - remove unnecessary MPI stuff
150     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
151     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
152       does not go over array-bounds and therefore returns reliable output.
153     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
154       this S/R has 4 output arguments, which are used inside "get_alarm";
155       when it is called with the same variable "ndum" in place of several
156       output arguments, this produces weird side effect inside "get_alarm"
157      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
158       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
159       address) and produces error.
160    o tools/gemake2: (March 27-29 2009)
161      with option "-mpi": link *_mpi files from "MODS" dir (this is what
162      testreport does).
163    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
164    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
165       update lab_sea.lsr & lab_sea.salt_plume results
166    o pkg/seaice:
167      Major overhaul of the LSOR solver: change discretization from original
168      finite differences to finite volume. The old routine is still in the
169      file seaice_lsr.F and can be turned on with the CPP-flag
170      SEAICE_OLD_AND_BAD_DISCRETIZATION
171      Along with this change, the discretization of the strain rates is changed.
172      The same flag turns on the old discretization in seaice_calc_strainrates.F
173      All verification experiments with seaice are affected (except for
174      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
175      results by setting the above flag.
176      Further changes involve changes in defaults:
177      - ALLOW_FLOODING is defined and turned on by default
178      - SEAICEadvSnow = .true. is now the default
179      - SEAICEadvSalt = .true. is now the default
180      - SEAICEadvAge  = .true. is now the default
181      - SEAICE_clipVelocities  = .false. is now the default
182                                         (as per J. Zhang's recommendation)
183      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
184        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
185      - seaice_growth: replace computation of UG by a simple copy from wspeed
186    
187    checkpoint61k
188    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
189      seaice_lsr: fixed a few metric terms,
190                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
191                  add more debugging diagnostics
192      seaice_evp: removed superfluous many metric terms of FV discretization
193                  of stress divergence
194                  affects lab_sea, lab_sea.hb87
195      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
196                  of stress divergence for non-evp solver
197                  (this part is not tested anywhere)
198      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
199                  they were effectively only half slip
200                  affects lab_sea.hb87
201      updated all relevant verification experiments (except lab_sea//output_adm.txt
202        which was left over, but fails at level 7 & 6)
203    
204    checkpoint61j
205    o pkg/seaice: turn a few hard wired parameters into run time parameters
206    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
207      time in seconds as promised by the usints in seaice_monitor and exf_monitor
208    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
209      that are not cubed-sphere grids
210    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
211    o pkg/ctrl:
212      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
213    o non-hydrostatic (calc_gw.F):
214      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
215      update output of exp. global_ocean.cs32x15.viscA4
216    o remove backward compatibility for thetaMin,phiMin
217      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
218    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
219      interpolated wind field not only for curvilineargrid=.true., but also
220      for a rotated grid (rotateGrid=.true.)
221    o pkg/exf: add capability to bypass interpolation for runoff
222      by setting yet another CPP-flag
223    o eesupp/src, B-grid exchange:
224      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
225    o autodiff
226      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
227      allows to switch to single-prec common blocks;
228      corresponding switch occurs in tamc.h, integer isbyte
229      TAF store directivs "byte" and "kind" seem equivalent;
230      Most tamc.h have been updated correspondingly.
231    
232    checkpoint61i
233    o autodiff:
234      fix autodiff_sore/_restore indices for obcs
235      (spotted by I. Hoteit, M. Mazloff)
236    o pkg/autodiff, pkg/ctrl:
237      Add flag to reduce all tapelev I/O to single-prec.
238      In data.ctrl set
239        doSinglePrecTapelev = .TRUE.
240    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
241      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
242    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
243      real fresh water flux (not yet)
244    o pkg/mdsio & rw:
245     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
246     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
247    o pkg/flt:
248     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
249       init_fixed & ini_varia.
250     - clean-up & simplify linear interpolation S/R:
251       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
252     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
253     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
254     - add vert. coordinate & horiz. indices to output files.
255     - change vertical position in initial condition, from index to depth [m].
256     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
257       (easier to get to a curvilinear grid) ; delX,delY no longer used.
258    o pkg/ggl90: a few modifications:
259     - fix bottom boundary condition, and interpolation of KappaE
260       near top and bottom
261     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
262     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
263     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
264    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
265      (maintain temporary backward compatibility, until next checkpoint)
266    
267    checkpoint61h
268    o pkg/diagnostics with "periodic averaging diagnostics":
269      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
270    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
271    o pkg/obcs: fix loop ranges for balancing code
272    o pkg/flt:
273     - improve criteria for finding which tile owns a float.
274     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
275    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
276      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
277      with ocean biogeo)
278    o pkg/flt:
279     - do some cleaning and fix the restart ;
280     - add output.txt in flt_example/results to get this pkg tested.
281    o genmake2: add an EXTENDED_SRC option and flag.
282       for now, cannot be turned on on command line (only through genmake_local)
283    o pkg/mdsio: read/write vector:
284     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
285     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
286       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
287     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
288      (drop to 4 digits matching for grad). But this test does not look very
289      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
290    
291    checkpoint61g
292    o pkg/flt:
293      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
294       + make OPTIONS file more standard.
295      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
296      - fix _BYTESWAPIO CPP-Flag
297      - standard reading of file-parameter "data.flt"
298      - fix argument list of S/R FLT_RESTART
299      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
300    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
301    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
302      a still unfixed compiler/optimization bug
303    
304    checkpoint61f
305    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
306      update results of global_ocean.cs32x15.icedyn test.
307    o move getcon.F from model/src to pkg/fizhi.
308    o pkg/exf: add parameter for extrapolation of temp up to the surface
309       and option to prevent negative evap (in bulk_largeyeager04 only).
310    o Prather Advection scheme: fix tracer conservation for divergent flow
311      (e.g., when using NonLin Free-Surface).
312    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
313    o gmredi (Visbeck-variable-K):
314     - add more parameters to Visbeck-variable-K.
315     - use a 5 points average for dSigmaR in Visbeck-K calculation
316       (more "homogenous": same stencil and same weights as in dSigmaH)
317     - update output of ideal_2D_oce experiment.
318    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
319      (#undef REAL4_IS_SLOW)
320     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
321       coordinate variable
322     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
323       (surface forcing fields), removes some of the functionality
324     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
325     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
326       probably not all: copy _RS surface flux fields to RL field before
327       calling DIAGNOSTICS_FILL
328     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
329       real*4 (CALL EXCH_*_RS) versions.
330     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
331       (generate new output).
332    
333    checkpoint61e
334    o gmredi (Visbeck-variable-K):
335      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
336      - change computation of Visbeck-K where Slope > Smax :        
337        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
338        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
339    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
340      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
341    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
342    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
343      does not become too large (to avoid precision problems in implicit-diffusion
344      solver); update ideal_2D_oce output.
345    o pkg ggl90:
346      - in ggl90_cal.F: compute only one set of visc/diff, used to
347        step forward TKE/T/S/momentum
348      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
349        have Prandlt =1)
350    o gmredi (fm07):
351      - add lower limit on Transition layer thickness + lower limit on 1/lambda
352      - allow to set few more params from data.gmredi
353    o pkg ggl90:
354          - add missing sqrt(2) factor in computation of mixing length
355            scale in ggl90_calc.F
356            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
357    
358    checkpoint61d
359    o adjoint modifs
360      - adapt to new field rhoInSitu
361      - allow to revert from StoreDynVars2D, StoreDynVars3D
362        to individual fields
363        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
364    o store 3-D (in-situ) density in commom block (DYNVARS.h)
365     - save 1 rho computation.
366     - no longer modify T & S inland when using down_slope pkg.
367    o gad_som : allow to switch to SOM advection for T & S without corresponding
368      pickup files (using new S/R: MDS_CHECK4FILE).
369    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
370      (for useSingleCpuIO to work in multi-threaded)
371    o pkg/shelfice:
372     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
373       with SHELFICEtopoFile in data.shelfice
374     - move code for reading ice shelf topography and modifying hFacC into separate
375       subroutines of the shelfice package
376     - separate initialisation of "fixed" and "variable" variables
377     - kTopC is not (yet) replaced by kSurfC, although this is possible
378    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
379    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
380      and rename:
381      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
382      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
383    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
384    
385    checkpoint61c
386    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
387      to add mass source/sink of fluid in the interior (3-D generalisation
388      of oceanic real-fresh water flux).
389    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
390    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
391    o new pkg: down_slope
392      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
393      - presently, modify T & S inland (dwnslp_calc_rho.F).
394        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
395      - implementation for ocean in P-coords not tested.
396      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
397    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
398      (to facilitate conversion of oceanic pkg to p-coordinate).
399    o change FIND_RHO to FIND_RHO_2D :
400      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
401    o new pkg: cheapaml
402    
403    checkpoint61b
404    o exch2:
405      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
406      - no longer depend on the order sequence (N,S,E,W).
407      - 3rd exchange no longer needed (tested with 24 tiles).
408      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
409      - exch_UV_A-grid readily available (but not yet tested).
410      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
411      (both are no longer needed) in exch_uv: no effect in forward run; but
412       get truncation error differences with adjoint exch.
413    o exch2:
414     - change index-bounds storage (moved from target to local tile,
415       more intuitive this way) ; rename/remove some variables.
416     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
417    
418    checkpoint61a
419    o exch2/matlab-topology-generator:
420      fix bug in index bounds for N-S internal exchange (hard to tell if this
421      had any effect on the solution).
422    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
423      is exceeded
424    o testreport: modify syntax of awk, so that it works also with
425      awk, and not only with nawk and gawk
426    
427    checkpoint61
428    o autodiff
429      Change default for TAF usage by removing argument '-nonew_arg'
430      This changes TAF subroutine argument list (ordering of active var.)
431      Omission of this flag leads to incompatibility w.r.t. TAMC
432      To restore TAMC-compatibility, need following modifs:
433      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
434      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
435      Tested TAF version is 1.9.22
436      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
437    
438    checkpoint60
439    --->>> This is the last checkpoint for which generating the adjoint
440    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
441    --->>> by default.
442    --->>> Future checkpoints will ommit this flag by default.
443    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
444    o pkg/grdchk: Add gradient check to etan0 perturbations.
445    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
446    o pkg/autodiff: more flexibility in zeroadj.
447      model/src: modifying do_oceanic_phys.F accordingly.
448    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
449    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
450      special setup of gmredi for which the adjoint is stable
451      enough for parameter optimization.
452    o bridging the gap between eddy stress and GM.
453      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
454          along with a change in CPP option (now ALLOW_EDDYPSI).
455      -> when using GM w/ GM_AdvForm:
456          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
457          is applied either in the tracer Eq. or in momentum Eq.
458          depending on data.gmredi (intro. GM_InMomAsStress).
459      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
460      The key modifications are in model/src/taueddy_external_forcing.F
461      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
462    
463    checkpoint59r
464    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
465      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
466      fix option to read coriolis(@ cell-corner) from files with CS-grid.
467    o pkg/mnc: add some attributes to standard 1D-coordinate variables
468    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
469      mass points, when using mnc for output
470      - add runtime parameter (missing_value, missing_value_int) to override
471        default (which is the value of getcon('UNDEF'))
472    o pkg/mnc: prepare mnc for the actual use of missing values with the
473      diagnostics package: small fix in mnc_cw_readwrite.template and more
474      initialisation of never used fields
475      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
476      versions
477    o pkg/thsice/thsice_ini_vars.F added default initial values so that
478      thermodynamics sea ice solver does not blow up when some initial fields
479      are missing.
480    o move from external_forcing_surf.F to ini_forcing.F
481      the p-coord. hack consisting in using pLoad to set phi0surf ;
482      update output of tutorial_global_oce_in_p (affected @ truncation level).
483    o Freshen up a bit hs94.1x64x5, notably:
484      remove rotationPeriod and tRef=5*0. (adjoint only), and add
485      exactConserv=.TRUE.
486    o pkg/generic_advdiff:
487      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
488      applies to files where Temperature & Salinity 2nd Order moments are used.
489    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
490      this uses a dynamically allocated internal state data structure
491      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
492      and requires a fortran 90 compiler
493    
494    checkpoint59q
495    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
496       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
497    o Refresh tutorial_global_oce_biogeo, notably:
498      - change bathymetry (put back seamounts in ACC, use hFacs)
499      - change EOS (POLY3 --> JMD95Z)
500      - use Bryan-Lewis vertical diffusivity
501      - use multidimensional advection
502      - remove old virtual virtual in dic pkg, now done through ptracer pkg
503      - change a couple of parameters in dic pkg
504    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
505    o pkg/obcs: change default to OBCSfixTopo = .true.,
506      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
507      - replace "debugMode" with "debugLevel .GE. debLevB"
508    o implementation of TAF directives for gchem,cfc,dic
509    o remove "exp5" (replaced by tutorial_deep_convection).
510    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
511      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
512      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
513      --> changes results in exp4, seaice_obcs
514    o tutorial_deep_convection :
515      update the set-up and increase resolution and domain size ; start
516      from pseudo initial conditions = output at t=120mn in order to see
517      something happening when running testreport.
518    o pkg/seaice: add os7mp as an advection scheme
519                  add check for advection schemes
520                  add a flag for restoring T and S underneath sea ice
521    o pkg/my82: add netcdf-support and diagnostics
522    o thsice pkg:
523      - Now hsMax limits snow height by turning it into ice following
524        flooding scheme (and now conserving energy)
525      - Slight rewriting of the formula in thsice_calc_thick.F
526      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
527      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
528    
529    checkpoint59p
530    o gchem / dic / cfc :
531      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
532      - add new parameter files: "data.dic" & "data.cfc" ;
533      - various re-arrangement in initialisation & header file ;
534      - fix tutorial_global_oce_biogeo for multi-threaded test.
535    o pkg/dic: test for "pickup_dic" file when restarting ;
536      if no pickup-file, can restart with a re-initialised pH (same as it did
537      before) providing pickupStrictlyMatch is set to False.
538    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
539      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
540    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
541      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
542    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
543     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
544       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
545    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
546       scheme to use for vorticty-term ;
547     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
548       (with default selectVortScheme, return to original discretisation)
549     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
550    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
551    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
552      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
553      also fix diagnostics VISCAHW & VISCA4W.
554    
555    checkpoint59o
556    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
557    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
558      move a few statemens out the main loop into separate loops
559    o pkg/shelfice:
560      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
561        (kg/m^2/s), does not break tests, because in verification/isomip,
562        rhoConstFresh=rhoConst (by accident)
563      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
564      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
565        new file model/src/seawater.F, so that they are available for all pkgs.
566      - convert potential temperature into in-situ temperature. This changes the
567        isomip tests => update tests
568    o add a flag writePickupAtEnd (default=true) to be able to suppress
569      writing a pickup at the last timestep
570    o tools/mpack-1.6 :
571      - disable automake (not working) and autoconf (not needed).
572      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
573        also cleaner with much less compilation warnings.
574    o pkg/profiles:
575      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
576      (for "less than 32 characters name" compiler requirement)
577    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
578      conditions that have a different sampling frequency than S/T/U/V obcs
579    o pkg/diagnostics (stats-diags):
580      - fix global Min/Max in case 1 processor get only empty tiles
581    o genmake2: replace (4 times)
582         make genmake_tc_1.o >> genmake_warnings 2>&1
583      with
584         COMM="$CC $CFLAGS -c genmake_tc_1.c"
585         echo $COMM >> genmake_warnings
586         $COMM >> genmake_warnings 2>&1
587      to make genmake2 always see the value of CC as specified in the optfile.
588    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
589      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
590      - modify verification advect_cs test to test SOM-advection on CS-grid.
591    o pkg/ctrl:
592      - Rewrite of ctrl_map_ini_ecco.F,
593        introducing a generic routine (ctrl_map_ini_gen.F).
594      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
595    
596    checkpoint59n
597    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
598      number in dedicate array "hdiag":
599      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
600        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
601      - many small changes (integer format) for large number of diagnostics
602      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
603        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
604    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
605      usingSphericalGrid, this allows to define the rotated grid coordinates
606      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
607      geographical coordinates according to the inverse of the rotation defined
608      by the Euler angles, so that Coriolis parameter and online-interpolation by
609      exf works with the geographical coordinates on XC/YC/XG/YG.
610      Naturally, this feature does not work with all packages, so some
611      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
612      profiles), because there the coordinates are assumed to be regular
613      spherical grid coordinates.
614    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
615      - introduce isopycnal diffusion coefficient control.
616    o tools/adjoint_options:
617      - additional control vector components.
618    o pkg/mnc: have mnc create marginally meaning full coordinate variables
619      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
620    o pkg/mypackage:
621      - add example of read/write pickup for state-var ;
622      - add entry points to the main code for state-vars diags & write-pickup.
623    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
624      transitions for useExfYearlyFields
625      - add new subroutine that determines the file to read from for
626        use*YearlyFields = .TRUE. and .FALSE.
627      - add a verification experiment to global_with_exf that tests
628        useExfYearlyFields with USE_EXF_INTERPOLATION defined
629    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
630      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
631      subroutines (which could be generated from a template, because they are
632      almost identical), for now they are included in obcs_prescribe_read.F for
633      simplicity
634    o pkg/exf:
635      - add a little more diagnostic to exf_interp_read (in analogy to
636        mds_read_field, can be turned off with debugLevel < debugLevA=1)
637      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
638        ugly but fast by unrolling short inner loops, inserting a unroll=8
639        directive in routine lagran, and splitting a loop and making do while the
640        outermost loop (the latter requires the intoduction of index arrays)
641    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
642    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
643      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
644    o verification/seaice_obcs: updated for restart test and latest options
645    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
646      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
647      for now this is only available for the C-grid code and also within
648      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
649    
650    checkpoint59m
651    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
652      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
653    o gad_som : fix flux output (& diagnostics) to have same units as other  
654      advection scheme fluxes (was previously multiplied by deltaT).  
655    o added verification/seaice_obcs both to test seaice open boundaries
656      and to provide an example matlab scrpt for generating them
657    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
658    o pkg/salt_plume: clean up salt_plume_frac.F to
659      remove redundancy in PlumeMethod 1 and 4
660    o pkg/kpp: added saltplume diagnostics
661    o pkg/obcs and pkg/seaice:
662      - do not set uice and vice to zero when OB*icefile are unspecified
663      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
664      - moved seaice tracer obcs after call to seaice_growth
665  o pkg/salt_plume: added various options for salt plume depth  o pkg/salt_plume: added various options for salt plume depth
666    criterion and for vertical distribution of the salt    criterion and for vertical distribution of the salt
667    
# Line 1926  o add two new packages Line 2584  o add two new packages
2584    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2585    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2586      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2587      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2588  o add offline package  o add offline package
2589  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2590    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

Legend:
Removed from v.1.928  
changed lines
  Added in v.1.1115

  ViewVC Help
Powered by ViewVC 1.1.22