/[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 1.938 by jmc, Mon Jan 14 02:29:20 2008 UTC revision 1.1111 by mlosch, Fri May 29 14:52:48 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/seaice:
8      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
9        of LSR (this change is expected to change the results slightly because now
10        it uses slightly difference moduli from the second last LSR solution, but
11        that is more consistent with the stress computations; this part of the code
12        is not tested in the verification experiments)
13      - fix diagnostics for flux of ice in case of B-grid
14      - turn strain rates eij and press into global fields within global
15        common block in SEAICE.h for more straighforward diagnostics
16      - fix diagnostics for principal stress components, press, zeta, eta
17        to give something meaning full
18    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
19      new output (all 4 tests) using default rotationPeriod.
20    o Fix computations of L4rdt in mom_calc_visc.F
21    o eesupp:
22      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
23      should be called before a "stop" if we know that all process are going
24      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
25    
26    checkpoint61o
27    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
28    o model/src/ini_curvilinear_grid.F:
29       compute angleSin/CosC when they are not read from a file
30    o pkg/seaice:
31       add pseudo time stepping for LSOR
32    o pkg/exch2:
33       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
34    o pkg/seaice:
35       Adding separate sea ice albedo, drag coefficients, and HO in Southern
36       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
37    o SingleCpuIO:
38       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
39    o pkg/seaice:
40       put exchanged variable in (local) common block for MPI+Multi-Threads
41       to work (necessary with exch1, and for now with exch2 too).
42    o verification: to get more experiments tested with mpi, mth and mpi+mth,
43      change tiling of:
44       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
45       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
46      update output of exp:
47       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
48       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
49      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
50                       (note: output.txt generated on faulks using only 1 tile)
51    o eesupp & mdsio (SingleCpuIO):
52     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
53       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
54       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
55     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
56     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
57       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
58    o pkg/exch2:
59     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
60       read parameter file "data.exch2" if it exists; otherwise try default regular
61       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
62     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
63       with new code (not to be used, just as a backup solution).
64     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
65       in utils/exch2/input.
66    
67    checkpoint61n
68    o eesupp & mdsio (SingleCpuIO):
69      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
70        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
71        receive real*4 array (instead of real*8) to read/write 32.bit files.
72        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
73         and remove new mapping S/R)
74    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
75      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
76        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
77        when using exch2. Add S/R to map global io-buffer to global model array.
78      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
79    
80    checkpoint61m
81    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
82      and add 3 other S/R for other types (R4,R8,RS).
83      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
84    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
85     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
86     - reduce number of macro definitions (keep only those which are used);
87       can always call directly the corrresponding S/R if needed.
88     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
89       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
90     Fixed wrong type of arg in:
91       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
92       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
93     To fix: global_sum of var in common block is wrong (multi-threaded) in:
94       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
95     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
96    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
97      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
98    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
99    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
100      edges are closed (zero depth); might happen with "blank tiles";
101      for now, disabled if using OBCS.
102    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
103      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
104    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
105      to reduce length of 1.D array print in STDOUT.
106    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
107      + use 48 tiles (16x8): this will allow to test "blank tiles".
108    o start to test MPI + multi-threaded (change testreport to skip tests
109      where number of tiles do not match).
110    o genmake2: add option "-omp" to turn on Open-MP ;
111      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
112    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
113      and keep the original tile numbering. Note: compatible with old
114      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
115    
116    checkpoint61l
117    o Overlaps had been forgotten in calculating ijk keys : fixed
118    o fix cyrus makedepend for gcc 4.4
119    o experiment fizhi-cs-aqualev20:
120      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
121      and generate new output. Note: new output is much closer to the old
122      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
123      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
124    o pkg/fizhi:
125     - change to avoid indices going deliberately over array-bounds
126     - remove unnecessary MPI stuff
127     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
128     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
129       does not go over array-bounds and therefore returns reliable output.
130     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
131       this S/R has 4 output arguments, which are used inside "get_alarm";
132       when it is called with the same variable "ndum" in place of several
133       output arguments, this produces weird side effect inside "get_alarm"
134      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
135       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
136       address) and produces error.
137    o tools/gemake2: (March 27-29 2009)
138      with option "-mpi": link *_mpi files from "MODS" dir (this is what
139      testreport does).
140    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
141    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
142       update lab_sea.lsr & lab_sea.salt_plume results
143    o pkg/seaice:
144      Major overhaul of the LSOR solver: change discretization from original
145      finite differences to finite volume. The old routine is still in the
146      file seaice_lsr.F and can be turned on with the CPP-flag
147      SEAICE_OLD_AND_BAD_DISCRETIZATION
148      Along with this change, the discretization of the strain rates is changed.
149      The same flag turns on the old discretization in seaice_calc_strainrates.F
150      All verification experiments with seaice are affected (except for
151      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
152      results by setting the above flag.
153      Further changes involve changes in defaults:
154      - ALLOW_FLOODING is defined and turned on by default
155      - SEAICEadvSnow = .true. is now the default
156      - SEAICEadvSalt = .true. is now the default
157      - SEAICEadvAge  = .true. is now the default
158      - SEAICE_clipVelocities  = .false. is now the default
159                                         (as per J. Zhang's recommendation)
160      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
161        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
162      - seaice_growth: replace computation of UG by a simple copy from wspeed
163    
164    checkpoint61k
165    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
166      seaice_lsr: fixed a few metric terms,
167                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
168                  add more debugging diagnostics
169      seaice_evp: removed superfluous many metric terms of FV discretization
170                  of stress divergence
171                  affects lab_sea, lab_sea.hb87
172      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
173                  of stress divergence for non-evp solver
174                  (this part is not tested anywhere)
175      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
176                  they were effectively only half slip
177                  affects lab_sea.hb87
178      updated all relevant verification experiments (except lab_sea//output_adm.txt
179        which was left over, but fails at level 7 & 6)
180    
181    checkpoint61j
182    o pkg/seaice: turn a few hard wired parameters into run time parameters
183    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
184      time in seconds as promised by the usints in seaice_monitor and exf_monitor
185    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
186      that are not cubed-sphere grids
187    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
188    o pkg/ctrl:
189      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
190    o non-hydrostatic (calc_gw.F):
191      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
192      update output of exp. global_ocean.cs32x15.viscA4
193    o remove backward compatibility for thetaMin,phiMin
194      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
195    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
196      interpolated wind field not only for curvilineargrid=.true., but also
197      for a rotated grid (rotateGrid=.true.)
198    o pkg/exf: add capability to bypass interpolation for runoff
199      by setting yet another CPP-flag
200    o eesupp/src, B-grid exchange:
201      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
202    o autodiff
203      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
204      allows to switch to single-prec common blocks;
205      corresponding switch occurs in tamc.h, integer isbyte
206      TAF store directivs "byte" and "kind" seem equivalent;
207      Most tamc.h have been updated correspondingly.
208    
209    checkpoint61i
210    o autodiff:
211      fix autodiff_sore/_restore indices for obcs
212      (spotted by I. Hoteit, M. Mazloff)
213    o pkg/autodiff, pkg/ctrl:
214      Add flag to reduce all tapelev I/O to single-prec.
215      In data.ctrl set
216        doSinglePrecTapelev = .TRUE.
217    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
218      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
219    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
220      real fresh water flux (not yet)
221    o pkg/mdsio & rw:
222     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
223     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
224    o pkg/flt:
225     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
226       init_fixed & ini_varia.
227     - clean-up & simplify linear interpolation S/R:
228       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
229     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
230     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
231     - add vert. coordinate & horiz. indices to output files.
232     - change vertical position in initial condition, from index to depth [m].
233     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
234       (easier to get to a curvilinear grid) ; delX,delY no longer used.
235    o pkg/ggl90: a few modifications:
236     - fix bottom boundary condition, and interpolation of KappaE
237       near top and bottom
238     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
239     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
240     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
241    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
242      (maintain temporary backward compatibility, until next checkpoint)
243    
244    checkpoint61h
245    o pkg/diagnostics with "periodic averaging diagnostics":
246      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
247    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
248    o pkg/obcs: fix loop ranges for balancing code
249    o pkg/flt:
250     - improve criteria for finding which tile owns a float.
251     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
252    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
253      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
254      with ocean biogeo)
255    o pkg/flt:
256     - do some cleaning and fix the restart ;
257     - add output.txt in flt_example/results to get this pkg tested.
258    o genmake2: add an EXTENDED_SRC option and flag.
259       for now, cannot be turned on on command line (only through genmake_local)
260    o pkg/mdsio: read/write vector:
261     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
262     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
263       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
264     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
265      (drop to 4 digits matching for grad). But this test does not look very
266      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
267    
268    checkpoint61g
269    o pkg/flt:
270      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
271       + make OPTIONS file more standard.
272      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
273      - fix _BYTESWAPIO CPP-Flag
274      - standard reading of file-parameter "data.flt"
275      - fix argument list of S/R FLT_RESTART
276      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
277    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
278    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
279      a still unfixed compiler/optimization bug
280    
281    checkpoint61f
282    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
283      update results of global_ocean.cs32x15.icedyn test.
284    o move getcon.F from model/src to pkg/fizhi.
285    o pkg/exf: add parameter for extrapolation of temp up to the surface
286       and option to prevent negative evap (in bulk_largeyeager04 only).
287    o Prather Advection scheme: fix tracer conservation for divergent flow
288      (e.g., when using NonLin Free-Surface).
289    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
290    o gmredi (Visbeck-variable-K):
291     - add more parameters to Visbeck-variable-K.
292     - use a 5 points average for dSigmaR in Visbeck-K calculation
293       (more "homogenous": same stencil and same weights as in dSigmaH)
294     - update output of ideal_2D_oce experiment.
295    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
296      (#undef REAL4_IS_SLOW)
297     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
298       coordinate variable
299     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
300       (surface forcing fields), removes some of the functionality
301     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
302     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
303       probably not all: copy _RS surface flux fields to RL field before
304       calling DIAGNOSTICS_FILL
305     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
306       real*4 (CALL EXCH_*_RS) versions.
307     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
308       (generate new output).
309    
310    checkpoint61e
311    o gmredi (Visbeck-variable-K):
312      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
313      - change computation of Visbeck-K where Slope > Smax :        
314        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
315        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
316    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
317      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
318    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
319    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
320      does not become too large (to avoid precision problems in implicit-diffusion
321      solver); update ideal_2D_oce output.
322    o pkg ggl90:
323      - in ggl90_cal.F: compute only one set of visc/diff, used to
324        step forward TKE/T/S/momentum
325      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
326        have Prandlt =1)
327    o gmredi (fm07):
328      - add lower limit on Transition layer thickness + lower limit on 1/lambda
329      - allow to set few more params from data.gmredi
330    o pkg ggl90:
331          - add missing sqrt(2) factor in computation of mixing length
332            scale in ggl90_calc.F
333            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
334    
335    checkpoint61d
336    o adjoint modifs
337      - adapt to new field rhoInSitu
338      - allow to revert from StoreDynVars2D, StoreDynVars3D
339        to individual fields
340        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
341    o store 3-D (in-situ) density in commom block (DYNVARS.h)
342     - save 1 rho computation.
343     - no longer modify T & S inland when using down_slope pkg.
344    o gad_som : allow to switch to SOM advection for T & S without corresponding
345      pickup files (using new S/R: MDS_CHECK4FILE).
346    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
347      (for useSingleCpuIO to work in multi-threaded)
348    o pkg/shelfice:
349     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
350       with SHELFICEtopoFile in data.shelfice
351     - move code for reading ice shelf topography and modifying hFacC into separate
352       subroutines of the shelfice package
353     - separate initialisation of "fixed" and "variable" variables
354     - kTopC is not (yet) replaced by kSurfC, although this is possible
355    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
356    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
357      and rename:
358      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
359      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
360    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
361    
362    checkpoint61c
363    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
364      to add mass source/sink of fluid in the interior (3-D generalisation
365      of oceanic real-fresh water flux).
366    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
367    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
368    o new pkg: down_slope
369      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
370      - presently, modify T & S inland (dwnslp_calc_rho.F).
371        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
372      - implementation for ocean in P-coords not tested.
373      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
374    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
375      (to facilitate conversion of oceanic pkg to p-coordinate).
376    o change FIND_RHO to FIND_RHO_2D :
377      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
378    o new pkg: cheapaml
379    
380    checkpoint61b
381    o exch2:
382      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
383      - no longer depend on the order sequence (N,S,E,W).
384      - 3rd exchange no longer needed (tested with 24 tiles).
385      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
386      - exch_UV_A-grid readily available (but not yet tested).
387      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
388      (both are no longer needed) in exch_uv: no effect in forward run; but
389       get truncation error differences with adjoint exch.
390    o exch2:
391     - change index-bounds storage (moved from target to local tile,
392       more intuitive this way) ; rename/remove some variables.
393     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
394    
395    checkpoint61a
396    o exch2/matlab-topology-generator:
397      fix bug in index bounds for N-S internal exchange (hard to tell if this
398      had any effect on the solution).
399    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
400      is exceeded
401    o testreport: modify syntax of awk, so that it works also with
402      awk, and not only with nawk and gawk
403    
404    checkpoint61
405    o autodiff
406      Change default for TAF usage by removing argument '-nonew_arg'
407      This changes TAF subroutine argument list (ordering of active var.)
408      Omission of this flag leads to incompatibility w.r.t. TAMC
409      To restore TAMC-compatibility, need following modifs:
410      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
411      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
412      Tested TAF version is 1.9.22
413      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
414    
415    checkpoint60
416    --->>> This is the last checkpoint for which generating the adjoint
417    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
418    --->>> by default.
419    --->>> Future checkpoints will ommit this flag by default.
420    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
421    o pkg/grdchk: Add gradient check to etan0 perturbations.
422    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
423    o pkg/autodiff: more flexibility in zeroadj.
424      model/src: modifying do_oceanic_phys.F accordingly.
425    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
426    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
427      special setup of gmredi for which the adjoint is stable
428      enough for parameter optimization.
429    o bridging the gap between eddy stress and GM.
430      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
431          along with a change in CPP option (now ALLOW_EDDYPSI).
432      -> when using GM w/ GM_AdvForm:
433          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
434          is applied either in the tracer Eq. or in momentum Eq.
435          depending on data.gmredi (intro. GM_InMomAsStress).
436      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
437      The key modifications are in model/src/taueddy_external_forcing.F
438      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
439    
440    checkpoint59r
441    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
442      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
443      fix option to read coriolis(@ cell-corner) from files with CS-grid.
444    o pkg/mnc: add some attributes to standard 1D-coordinate variables
445    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
446      mass points, when using mnc for output
447      - add runtime parameter (missing_value, missing_value_int) to override
448        default (which is the value of getcon('UNDEF'))
449    o pkg/mnc: prepare mnc for the actual use of missing values with the
450      diagnostics package: small fix in mnc_cw_readwrite.template and more
451      initialisation of never used fields
452      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
453      versions
454    o pkg/thsice/thsice_ini_vars.F added default initial values so that
455      thermodynamics sea ice solver does not blow up when some initial fields
456      are missing.
457    o move from external_forcing_surf.F to ini_forcing.F
458      the p-coord. hack consisting in using pLoad to set phi0surf ;
459      update output of tutorial_global_oce_in_p (affected @ truncation level).
460    o Freshen up a bit hs94.1x64x5, notably:
461      remove rotationPeriod and tRef=5*0. (adjoint only), and add
462      exactConserv=.TRUE.
463    o pkg/generic_advdiff:
464      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
465      applies to files where Temperature & Salinity 2nd Order moments are used.
466    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
467      this uses a dynamically allocated internal state data structure
468      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
469      and requires a fortran 90 compiler
470    
471    checkpoint59q
472    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
473       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
474    o Refresh tutorial_global_oce_biogeo, notably:
475      - change bathymetry (put back seamounts in ACC, use hFacs)
476      - change EOS (POLY3 --> JMD95Z)
477      - use Bryan-Lewis vertical diffusivity
478      - use multidimensional advection
479      - remove old virtual virtual in dic pkg, now done through ptracer pkg
480      - change a couple of parameters in dic pkg
481    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
482    o pkg/obcs: change default to OBCSfixTopo = .true.,
483      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
484      - replace "debugMode" with "debugLevel .GE. debLevB"
485    o implementation of TAF directives for gchem,cfc,dic
486    o remove "exp5" (replaced by tutorial_deep_convection).
487    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
488      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
489      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
490      --> changes results in exp4, seaice_obcs
491    o tutorial_deep_convection :
492      update the set-up and increase resolution and domain size ; start
493      from pseudo initial conditions = output at t=120mn in order to see
494      something happening when running testreport.
495    o pkg/seaice: add os7mp as an advection scheme
496                  add check for advection schemes
497                  add a flag for restoring T and S underneath sea ice
498    o pkg/my82: add netcdf-support and diagnostics
499    o thsice pkg:
500      - Now hsMax limits snow height by turning it into ice following
501        flooding scheme (and now conserving energy)
502      - Slight rewriting of the formula in thsice_calc_thick.F
503      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
504      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
505    
506    checkpoint59p
507    o gchem / dic / cfc :
508      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
509      - add new parameter files: "data.dic" & "data.cfc" ;
510      - various re-arrangement in initialisation & header file ;
511      - fix tutorial_global_oce_biogeo for multi-threaded test.
512    o pkg/dic: test for "pickup_dic" file when restarting ;
513      if no pickup-file, can restart with a re-initialised pH (same as it did
514      before) providing pickupStrictlyMatch is set to False.
515    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
516      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
517    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
518      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
519    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
520     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
521       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
522    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
523       scheme to use for vorticty-term ;
524     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
525       (with default selectVortScheme, return to original discretisation)
526     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
527    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
528    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
529      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
530      also fix diagnostics VISCAHW & VISCA4W.
531    
532    checkpoint59o
533    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
534    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
535      move a few statemens out the main loop into separate loops
536    o pkg/shelfice:
537      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
538        (kg/m^2/s), does not break tests, because in verification/isomip,
539        rhoConstFresh=rhoConst (by accident)
540      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
541      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
542        new file model/src/seawater.F, so that they are available for all pkgs.
543      - convert potential temperature into in-situ temperature. This changes the
544        isomip tests => update tests
545    o add a flag writePickupAtEnd (default=true) to be able to suppress
546      writing a pickup at the last timestep
547    o tools/mpack-1.6 :
548      - disable automake (not working) and autoconf (not needed).
549      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
550        also cleaner with much less compilation warnings.
551    o pkg/profiles:
552      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
553      (for "less than 32 characters name" compiler requirement)
554    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
555      conditions that have a different sampling frequency than S/T/U/V obcs
556    o pkg/diagnostics (stats-diags):
557      - fix global Min/Max in case 1 processor get only empty tiles
558    o genmake2: replace (4 times)
559         make genmake_tc_1.o >> genmake_warnings 2>&1
560      with
561         COMM="$CC $CFLAGS -c genmake_tc_1.c"
562         echo $COMM >> genmake_warnings
563         $COMM >> genmake_warnings 2>&1
564      to make genmake2 always see the value of CC as specified in the optfile.
565    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
566      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
567      - modify verification advect_cs test to test SOM-advection on CS-grid.
568    o pkg/ctrl:
569      - Rewrite of ctrl_map_ini_ecco.F,
570        introducing a generic routine (ctrl_map_ini_gen.F).
571      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
572    
573    checkpoint59n
574    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
575      number in dedicate array "hdiag":
576      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
577        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
578      - many small changes (integer format) for large number of diagnostics
579      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
580        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
581    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
582      usingSphericalGrid, this allows to define the rotated grid coordinates
583      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
584      geographical coordinates according to the inverse of the rotation defined
585      by the Euler angles, so that Coriolis parameter and online-interpolation by
586      exf works with the geographical coordinates on XC/YC/XG/YG.
587      Naturally, this feature does not work with all packages, so some
588      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
589      profiles), because there the coordinates are assumed to be regular
590      spherical grid coordinates.
591    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
592      - introduce isopycnal diffusion coefficient control.
593    o tools/adjoint_options:
594      - additional control vector components.
595    o pkg/mnc: have mnc create marginally meaning full coordinate variables
596      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
597    o pkg/mypackage:
598      - add example of read/write pickup for state-var ;
599      - add entry points to the main code for state-vars diags & write-pickup.
600    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
601      transitions for useExfYearlyFields
602      - add new subroutine that determines the file to read from for
603        use*YearlyFields = .TRUE. and .FALSE.
604      - add a verification experiment to global_with_exf that tests
605        useExfYearlyFields with USE_EXF_INTERPOLATION defined
606    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
607      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
608      subroutines (which could be generated from a template, because they are
609      almost identical), for now they are included in obcs_prescribe_read.F for
610      simplicity
611    o pkg/exf:
612      - add a little more diagnostic to exf_interp_read (in analogy to
613        mds_read_field, can be turned off with debugLevel < debugLevA=1)
614      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
615        ugly but fast by unrolling short inner loops, inserting a unroll=8
616        directive in routine lagran, and splitting a loop and making do while the
617        outermost loop (the latter requires the intoduction of index arrays)
618    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
619    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
620      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
621    o verification/seaice_obcs: updated for restart test and latest options
622    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
623      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
624      for now this is only available for the C-grid code and also within
625      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
626    
627  checkpoint59m  checkpoint59m
628  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)  o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
629    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature    and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
# Line 1941  o add two new packages Line 2561  o add two new packages
2561    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2562    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2563      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2564      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2565  o add offline package  o add offline package
2566  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2567    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

Legend:
Removed from v.1.938  
changed lines
  Added in v.1.1111

  ViewVC Help
Powered by ViewVC 1.1.22