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revision 1.1004 by heimbach, Thu Jun 19 16:43:56 2008 UTC revision 1.1050 by dfer, Mon Jan 5 16:40:50 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 Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
8      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
9      with ocean biogeo)
10    o pkg/flt:
11     - do some cleaning and fix the restart ;
12     - add output.txt in flt_example/results to get this pkg tested.
13    o genmake2: add an EXTENDED_SRC option and flag.
14       for now, cannot be turned on on command line (only through genmake_local)
15    o pkg/mdsio: read/write vector:
16     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
17     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
18       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
19     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
20      (drop to 4 digits matching for grad). But this test does not look very
21      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
22    
23    checkpoint61g
24    o pkg/flt:
25      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
26       + make OPTIONS file more standard.
27      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
28      - fix _BYTESWAPIO CPP-Flag
29      - standard reading of file-parameter "data.flt"
30      - fix argument list of S/R FLT_RESTART
31      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
32    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
33    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
34      a still unfixed compiler/optimization bug
35    
36    checkpoint61f
37    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
38      update results of global_ocean.cs32x15.icedyn test.
39    o move getcon.F from model/src to pkg/fizhi.
40    o pkg/exf: add parameter for extrapolation of temp up to the surface
41       and option to prevent negative evap (in bulk_largeyeager04 only).
42    o Prather Advection scheme: fix tracer conservation for divergent flow
43      (e.g., when using NonLin Free-Surface).
44    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
45    o gmredi (Visbeck-variable-K):
46     - add more parameters to Visbeck-variable-K.
47     - use a 5 points average for dSigmaR in Visbeck-K calculation
48       (more "homogenous": same stencil and same weights as in dSigmaH)
49     - update output of ideal_2D_oce experiment.
50    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
51      (#undef REAL4_IS_SLOW)
52     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
53       coordinate variable
54     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
55       (surface forcing fields), removes some of the functionality
56     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
57     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
58       probably not all: copy _RS surface flux fields to RL field before
59       calling DIAGNOSTICS_FILL
60     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
61       real*4 (CALL EXCH_*_RS) versions.
62     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
63       (generate new output).
64    
65    checkpoint61e
66    o gmredi (Visbeck-variable-K):
67      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
68      - change computation of Visbeck-K where Slope > Smax :        
69        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
70        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
71    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
72      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
73    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
74    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
75      does not become too large (to avoid precision problems in implicit-diffusion
76      solver); update ideal_2D_oce output.
77    o pkg ggl90:
78      - in ggl90_cal.F: compute only one set of visc/diff, used to
79        step forward TKE/T/S/momentum
80      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
81        have Prandlt =1)
82    o gmredi (fm07):
83      - add lower limit on Transition layer thickness + lower limit on 1/lambda
84      - allow to set few more params from data.gmredi
85    o pkg ggl90:
86          - add missing sqrt(2) factor in computation of mixing length
87            scale in ggl90_calc.F
88            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
89    
90    checkpoint61d
91    o adjoint modifs
92      - adapt to new field rhoInSitu
93      - allow to revert from StoreDynVars2D, StoreDynVars3D
94        to individual fields
95        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
96    o store 3-D (in-situ) density in commom block (DYNVARS.h)
97     - save 1 rho computation.
98     - no longer modify T & S inland when using down_slope pkg.
99    o gad_som : allow to switch to SOM advection for T & S without corresponding
100      pickup files (using new S/R: MDS_CHECK4FILE).
101    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
102      (for useSingleCpuIO to work in multi-threaded)
103    o pkg/shelfice:
104     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
105       with SHELFICEtopoFile in data.shelfice
106     - move code for reading ice shelf topography and modifying hFacC into separate
107       subroutines of the shelfice package
108     - separate initialisation of "fixed" and "variable" variables
109     - kTopC is not (yet) replaced by kSurfC, although this is possible
110    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
111    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
112      and rename:
113      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
114      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
115    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
116    
117    checkpoint61c
118    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
119      to add mass source/sink of fluid in the interior (3-D generalisation
120      of oceanic real-fresh water flux).
121    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
122    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
123    o new pkg: down_slope
124      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
125      - presently, modify T & S inland (dwnslp_calc_rho.F).
126        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
127      - implementation for ocean in P-coords not tested.
128      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
129    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
130      (to facilitate conversion of oceanic pkg to p-coordinate).
131    o change FIND_RHO to FIND_RHO_2D :
132      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
133    o new pkg: cheapaml
134    
135    checkpoint61b
136    o exch2:
137      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
138      - no longer depend on the order sequence (N,S,E,W).
139      - 3rd exchange no longer needed (tested with 24 tiles).
140      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
141      - exch_UV_A-grid readily available (but not yet tested).
142      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
143      (both are no longer needed) in exch_uv: no effect in forward run; but
144       get truncation error differences with adjoint exch.
145    o exch2:
146     - change index-bounds storage (moved from target to local tile,
147       more intuitive this way) ; rename/remove some variables.
148     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
149    
150    checkpoint61a
151    o exch2/matlab-topology-generator:
152      fix bug in index bounds for N-S internal exchange (hard to tell if this
153      had any effect on the solution).
154    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
155      is exceeded
156    o testreport: modify syntax of awk, so that it works also with
157      awk, and not only with nawk and gawk
158    
159    checkpoint61
160    o autodiff
161      Change default for TAF usage by removing argument '-nonew_arg'
162      This changes TAF subroutine argument list (ordering of active var.)
163      Omission of this flag leads to incompatibility w.r.t. TAMC
164      To restore TAMC-compatibility, need following modifs:
165      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
166      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
167      Tested TAF version is 1.9.22
168      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
169    
170  checkpoint60  checkpoint60
171  --->>> This is the last checkpoint for which generating the adjoint  --->>> This is the last checkpoint for which generating the adjoint
172  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"  --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"

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