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revision 1.1002 by gforget, Wed Jun 11 19:32:27 2008 UTC revision 1.1081 by mlosch, Fri Mar 20 16:04:38 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      Major overhaul of the LSOR solver: change discretization from original
9      finite differences to finite volume. The old routine is still in the
10      file seaice_lsr.F and can be turned on with the CPP-flag
11      SEAICE_OLD_AND_BAD_DISCRETIZATION
12      Along with this change, the discretization of the strain rates is changed.
13      The same flag turns on the old discretization in seaice_calc_strainrates.F
14      All verification experiments with seaice are affected (except for
15      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
16      results by setting the above flag.
17      Further changes involve changes in defaults:
18      - ALLOW_FLOODING is defined and turned on by default
19      - SEAICE_advSnow = .true. is now the default
20      - SEAICE_advSalt = .true. is now the default
21      - SEAICE_advAge  = .true. is now the default
22      - SEAICE_clipVelocities  = .false. is now the default
23                                         (as per J. Zhang's recommendation)
24      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
25        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
26      - seaice_growth: replace computation of UG by a simple copy from wspeed
27    
28    checkpoint61k
29    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
30      seaice_lsr: fixed a few metric terms,
31                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
32                  add more debugging diagnostics
33      seaice_evp: removed superfluous many metric terms of FV discretization
34                  of stress divergence
35                  affects lab_sea, lab_sea.hb87
36      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
37                  of stress divergence for non-evp solver
38                  (this part is not tested anywhere)
39      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
40                  they were effectively only half slip
41                  affects lab_sea.hb87
42      updated all relevant verification experiments
43    
44    checkpoint61j
45    o pkg/seaice: turn a few hard wired parameters into run time parameters
46    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
47      time in seconds as promised by the usints in seaice_monitor and exf_monitor
48    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
49      that are not cubed-sphere grids
50    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
51    o pkg/ctrl:
52      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
53    o non-hydrostatic (calc_gw.F):
54      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
55      update output of exp. global_ocean.cs32x15.viscA4
56    o remove backward compatibility for thetaMin,phiMin
57      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
58    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
59      interpolated wind field not only for curvilineargrid=.true., but also
60      for a rotated grid (rotateGrid=.true.)
61    o pkg/exf: add capability to bypass interpolation for runoff
62      by setting yet another CPP-flag
63    o eesupp/src, B-grid exchange:
64      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
65    o autodiff
66      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
67      allows to switch to single-prec common blocks;
68      corresponding switch occurs in tamc.h, integer isbyte
69      TAF store directivs "byte" and "kind" seem equivalent;
70      Most tamc.h have been updated correspondingly.
71    
72    checkpoint61i
73    o autodiff:
74      fix autodiff_sore/_restore indices for obcs
75      (spotted by I. Hoteit, M. Mazloff)
76    o pkg/autodiff, pkg/ctrl:
77      Add flag to reduce all tapelev I/O to single-prec.
78      In data.ctrl set
79        doSinglePrecTapelev = .TRUE.
80    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
81      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
82    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
83      real fresh water flux (not yet)
84    o pkg/mdsio & rw:
85     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
86     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
87    o pkg/flt:
88     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
89       init_fixed & ini_varia.
90     - clean-up & simplify linear interpolation S/R:
91       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
92     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
93     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
94     - add vert. coordinate & horiz. indices to output files.
95     - change vertical position in initial condition, from index to depth [m].
96     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
97       (easier to get to a curvilinear grid) ; delX,delY no longer used.
98    o pkg/ggl90: a few modifications:
99     - fix bottom boundary condition, and interpolation of KappaE
100       near top and bottom
101     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
102     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
103     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
104    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
105      (maintain temporary backward compatibility, until next checkpoint)
106    
107    checkpoint61h
108    o pkg/diagnostics with "periodic averaging diagnostics":
109      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
110    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
111    o pkg/obcs: fix loop ranges for balancing code
112    o pkg/flt:
113     - improve criteria for finding which tile owns a float.
114     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
115    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
116      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
117      with ocean biogeo)
118    o pkg/flt:
119     - do some cleaning and fix the restart ;
120     - add output.txt in flt_example/results to get this pkg tested.
121    o genmake2: add an EXTENDED_SRC option and flag.
122       for now, cannot be turned on on command line (only through genmake_local)
123    o pkg/mdsio: read/write vector:
124     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
125     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
126       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
127     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
128      (drop to 4 digits matching for grad). But this test does not look very
129      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
130    
131    checkpoint61g
132    o pkg/flt:
133      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
134       + make OPTIONS file more standard.
135      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
136      - fix _BYTESWAPIO CPP-Flag
137      - standard reading of file-parameter "data.flt"
138      - fix argument list of S/R FLT_RESTART
139      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
140    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
141    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
142      a still unfixed compiler/optimization bug
143    
144    checkpoint61f
145    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
146      update results of global_ocean.cs32x15.icedyn test.
147    o move getcon.F from model/src to pkg/fizhi.
148    o pkg/exf: add parameter for extrapolation of temp up to the surface
149       and option to prevent negative evap (in bulk_largeyeager04 only).
150    o Prather Advection scheme: fix tracer conservation for divergent flow
151      (e.g., when using NonLin Free-Surface).
152    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
153    o gmredi (Visbeck-variable-K):
154     - add more parameters to Visbeck-variable-K.
155     - use a 5 points average for dSigmaR in Visbeck-K calculation
156       (more "homogenous": same stencil and same weights as in dSigmaH)
157     - update output of ideal_2D_oce experiment.
158    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
159      (#undef REAL4_IS_SLOW)
160     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
161       coordinate variable
162     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
163       (surface forcing fields), removes some of the functionality
164     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
165     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
166       probably not all: copy _RS surface flux fields to RL field before
167       calling DIAGNOSTICS_FILL
168     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
169       real*4 (CALL EXCH_*_RS) versions.
170     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
171       (generate new output).
172    
173    checkpoint61e
174    o gmredi (Visbeck-variable-K):
175      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
176      - change computation of Visbeck-K where Slope > Smax :        
177        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
178        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
179    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
180      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
181    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
182    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
183      does not become too large (to avoid precision problems in implicit-diffusion
184      solver); update ideal_2D_oce output.
185    o pkg ggl90:
186      - in ggl90_cal.F: compute only one set of visc/diff, used to
187        step forward TKE/T/S/momentum
188      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
189        have Prandlt =1)
190    o gmredi (fm07):
191      - add lower limit on Transition layer thickness + lower limit on 1/lambda
192      - allow to set few more params from data.gmredi
193    o pkg ggl90:
194          - add missing sqrt(2) factor in computation of mixing length
195            scale in ggl90_calc.F
196            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
197    
198    checkpoint61d
199    o adjoint modifs
200      - adapt to new field rhoInSitu
201      - allow to revert from StoreDynVars2D, StoreDynVars3D
202        to individual fields
203        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
204    o store 3-D (in-situ) density in commom block (DYNVARS.h)
205     - save 1 rho computation.
206     - no longer modify T & S inland when using down_slope pkg.
207    o gad_som : allow to switch to SOM advection for T & S without corresponding
208      pickup files (using new S/R: MDS_CHECK4FILE).
209    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
210      (for useSingleCpuIO to work in multi-threaded)
211    o pkg/shelfice:
212     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
213       with SHELFICEtopoFile in data.shelfice
214     - move code for reading ice shelf topography and modifying hFacC into separate
215       subroutines of the shelfice package
216     - separate initialisation of "fixed" and "variable" variables
217     - kTopC is not (yet) replaced by kSurfC, although this is possible
218    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
219    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
220      and rename:
221      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
222      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
223    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
224    
225    checkpoint61c
226    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
227      to add mass source/sink of fluid in the interior (3-D generalisation
228      of oceanic real-fresh water flux).
229    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
230    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
231    o new pkg: down_slope
232      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
233      - presently, modify T & S inland (dwnslp_calc_rho.F).
234        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
235      - implementation for ocean in P-coords not tested.
236      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
237    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
238      (to facilitate conversion of oceanic pkg to p-coordinate).
239    o change FIND_RHO to FIND_RHO_2D :
240      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
241    o new pkg: cheapaml
242    
243    checkpoint61b
244    o exch2:
245      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
246      - no longer depend on the order sequence (N,S,E,W).
247      - 3rd exchange no longer needed (tested with 24 tiles).
248      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
249      - exch_UV_A-grid readily available (but not yet tested).
250      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
251      (both are no longer needed) in exch_uv: no effect in forward run; but
252       get truncation error differences with adjoint exch.
253    o exch2:
254     - change index-bounds storage (moved from target to local tile,
255       more intuitive this way) ; rename/remove some variables.
256     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
257    
258    checkpoint61a
259    o exch2/matlab-topology-generator:
260      fix bug in index bounds for N-S internal exchange (hard to tell if this
261      had any effect on the solution).
262    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
263      is exceeded
264    o testreport: modify syntax of awk, so that it works also with
265      awk, and not only with nawk and gawk
266    
267    checkpoint61
268    o autodiff
269      Change default for TAF usage by removing argument '-nonew_arg'
270      This changes TAF subroutine argument list (ordering of active var.)
271      Omission of this flag leads to incompatibility w.r.t. TAMC
272      To restore TAMC-compatibility, need following modifs:
273      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
274      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
275      Tested TAF version is 1.9.22
276      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
277    
278    checkpoint60
279    --->>> This is the last checkpoint for which generating the adjoint
280    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
281    --->>> by default.
282    --->>> Future checkpoints will ommit this flag by default.
283    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
284  o pkg/grdchk: Add gradient check to etan0 perturbations.  o pkg/grdchk: Add gradient check to etan0 perturbations.
285  o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).  o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
286  o pkg/autodiff: more flexibility in zeroadj.  o pkg/autodiff: more flexibility in zeroadj.
# Line 22  o bridging the gap between eddy stress a Line 299  o bridging the gap between eddy stress a
299    -> ALLOW_EDDYPSI_CONTROL for estimation purpose.    -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
300    The key modifications are in model/src/taueddy_external_forcing.F    The key modifications are in model/src/taueddy_external_forcing.F
301    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F    pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
302    
303  checkpoint59r  checkpoint59r
304  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array  o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
305    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);    from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
# Line 2146  o add two new packages Line 2424  o add two new packages
2424    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2425    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2426      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2427      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2428  o add offline package  o add offline package
2429  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2430    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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