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$Header$ |
$Header$ |
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$Name$ |
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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o adjoint testing: in preparation for changing testreport: |
8 |
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- output format: cost and grad written on separated lines |
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- ad output results in directory "results" (instead of "results_ad") |
10 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
11 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
12 |
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o pkg/ecco: allow user defined cost function contributions |
13 |
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o testreport: |
14 |
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Allow to choose (per experiment) the list of tested output variables |
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and the main variable (used to issue a pass/FAIL ) ; |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
17 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
18 |
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Also modify printing of summary: |
19 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
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b) echo the list of tested variables in the individual summary.txt of |
21 |
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each experiment. |
22 |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
23 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
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(but still depend on the tile decompostion of the domain). |
25 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
26 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
27 |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
28 |
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the solution to the stress coupling issues with the B-grid. |
29 |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
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remove .cvsignore from input dir. (since testreport no longer run here). |
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o pkg/thsice: |
32 |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
33 |
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- fix reshaping of sea-ice just after advection: |
34 |
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melt all the ice only if ice-volume is too small. |
35 |
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- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
36 |
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prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
37 |
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and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
38 |
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o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
39 |
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tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
40 |
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o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
41 |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
42 |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
43 |
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and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
44 |
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of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
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-> update output.txt |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
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this affects truncation error: -> update output.txt of exp: |
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global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
49 |
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ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
50 |
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|
51 |
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checkpoint59f |
52 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
53 |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
54 |
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a bounded range (in forward mode) |
55 |
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o pkg/ecco, ctrl, autodiff and mom_common: |
56 |
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internal parameter controls, completements of implementations |
57 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
58 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
59 |
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(not seem any difference in testing results). |
60 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
61 |
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at face corners. |
62 |
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o pkg/generic_advdiff: |
63 |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
64 |
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loop range indices for computing vertical advection tendency |
65 |
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and do the calculation in the interior only (no overlap) ; |
66 |
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for now, only implemented for SOM advection (to save CPU time). |
67 |
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- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
68 |
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o exch2 adjoint |
69 |
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First set of changes: |
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- add exch2 hand-written adjoint templates |
71 |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
72 |
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This will require cleanup in pkg/autodiff/*.F |
73 |
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(changed routines currently kept separate in verif. code/) |
74 |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
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that used to hide exch2 or cubed-sphere specific code |
76 |
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(commented via 'cph-exch2') |
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o pkg/seaice |
78 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
79 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
80 |
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output of global_ocean.cs32x15.thsice . |
81 |
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|
82 |
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checkpoint59e |
83 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
84 |
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for B-grid vector (not yet tested) and C-grid vector (<- only used |
85 |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
86 |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
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(#ifdef ALLOW_SALT_PLUME) |
88 |
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o gather_2d/scatter_2d: removed halo regions |
89 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
90 |
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scheme and the corresponding test case (under front_relax dir). For now, |
91 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
92 |
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adjoint: store directives updated, but gradient checks deteriorated, |
93 |
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so maybe GM/Redi adjoint is now broken. |
94 |
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o seaice adjoint |
95 |
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* add AREA, HEFF, HSNOW as control variable |
96 |
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(should not change lab_sea results) |
97 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
98 |
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o pkg/seaice: |
99 |
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* added computation of saltFlux in seaice_growth; |
100 |
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For time being, sea ice salinity is assumed constant |
101 |
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contribution of snow flooding to freshening of sea ice is neglected. |
102 |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
103 |
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defaults to 0.0 in order to maintain backward compatibility. |
104 |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
105 |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
106 |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
107 |
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heat content used to melt or grow ice |
108 |
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* commented out cap of HICE: it helps keep ice thinner |
109 |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
110 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
111 |
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|
112 |
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checkpoint59d |
113 |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
114 |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
115 |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
116 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
117 |
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and change default value of parameter "GM_Small_Number"; |
118 |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
119 |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
120 |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
121 |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
122 |
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o pkg/ctrl: add forcingPrecond run time parameter |
123 |
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o pkg/seaice: |
124 |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
125 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
126 |
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changes verification/lab_sea |
127 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
128 |
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read, understand, and debug. This causes changes at the truncation level. |
129 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
130 |
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part) of the LSR solver. Changes all LSR results. |
131 |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
132 |
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is initilized with small values - does not change lab_sea results. |
133 |
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- added HsnowFile initialization capability |
134 |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
135 |
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initialization of pkg/smooth and application to control vector |
136 |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
137 |
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o dependencies: pkg/profiles requires pkg/cal |
138 |
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o pkg/profiles: |
139 |
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- added option ALLOW_PROFILES_GENERICGRID |
140 |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
141 |
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that interpolation information (grid points and coefficients) is provided |
142 |
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within the netcdf input files. |
143 |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
144 |
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that allow you to prepare netcdf input files. |
145 |
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- also modified: cleaner include statements, cleaner error print statements, |
146 |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
147 |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
148 |
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o pkg/seaice: |
149 |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
150 |
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requires a new routine: seaice_diagnostics_fill.F |
151 |
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- make sure that seaice does not move if not forced (pressure replacement |
152 |
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method, Hibler and Ip, 1995), changes results |
153 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
154 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
155 |
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It is turned off by default (=-1.), because it changes the results. |
156 |
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- make it possible to read AREA from a file, too. |
157 |
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|
158 |
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checkpoint59c |
159 |
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o add S/R and diagnostics for oceanic mixed-layer depth |
160 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
161 |
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o pkg/thsice: |
162 |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
163 |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
164 |
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o pkg/obcs: |
165 |
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- bug fix for balance code |
166 |
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o pkg/seaice: |
167 |
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- allow values of SEAICE_elasticParm > 1 |
168 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
169 |
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to SEAICE_elasticParm |
170 |
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- make lsr boundary conditions free slip (by default), changes result |
171 |
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- add code for no slip boundary conditions for lsr |
172 |
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- set minimum of zeta to zero (and not 4e8) (changes results) |
173 |
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- add a cap on AREA after advecting AREA if seaice_growth is not called |
174 |
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o change calculation of Visbeck K: |
175 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
176 |
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by GM_maxSlope). this is equivalent to what was comuted before with |
177 |
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clipping or linear tappering. |
178 |
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- fix vertical averaging (wrong by 1/2 level) |
179 |
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- leave the old version (but will not be maintained) within |
180 |
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#ifdef OLD_VISBECK_CALC / #endif |
181 |
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- update output of exp. ideal_2D_oce |
182 |
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o change error catch in calc_r_star to improve vectorization |
183 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
184 |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
185 |
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o adjoint: |
186 |
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Re-organized adjoint checkpointing according to Matt Mazloff |
187 |
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(but with modifs/completions/cleanups) |
188 |
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Storing is now bundled into large arrays to optimized I/O |
189 |
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(and second step in cleanup of the_main_loop) |
190 |
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|
191 |
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checkpoint59b |
192 |
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o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
193 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
194 |
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o pkg/seaice: |
195 |
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- get rid of three more exchanges seaice_calc_viscosities (required |
196 |
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different loop boundaries in seaice_lsr and seaice_ocean_stress) |
197 |
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- bug fix in seaice_ocean_stress (update of lab_sea required) |
198 |
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- reduce loop boundaries to necessary minimum also in seaice_evp |
199 |
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- go back to the old way of computing deltaC/Z as the adjoint likes that |
200 |
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better |
201 |
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o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
202 |
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passive tracer to an Age Tracer) + update output.txt |
203 |
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o pkg/exf: |
204 |
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- implement A-grid / C-grid selection for wind-stress input files. |
205 |
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- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
206 |
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for now, in exf_bulk_largeyeager04.F only : |
207 |
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- change implementation for case where windspeed + 2. components wind-stress |
208 |
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are read-in. AND use rhoConstFresh to convert evap. |
209 |
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o pkg/seaice: |
210 |
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- use correct EXCH_UV for wind-forcing (on A-grid). |
211 |
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- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
212 |
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SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
213 |
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o pkg/exf: |
214 |
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- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
215 |
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EXF_INTERPOLATION: |
216 |
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- merge global_with_exf/code version of exf_interp_read.F |
217 |
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to the main code ; |
218 |
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- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
219 |
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reading the file ; Important: This options needs to be defined to recover |
220 |
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previous code. |
221 |
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otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
222 |
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- no longer loose real*8 precision along the way when using exf_iprec=64. |
223 |
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o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
224 |
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- change discretisation of evp-solver in order to avoid another exchange |
225 |
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(changes lab_sea) and clean up a little |
226 |
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- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
227 |
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help the adjoint (this also changes the results slightly) |
228 |
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- add a few "_d 0" where they had been missing in seaice_evp.F |
229 |
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- cleaning up: remove unused seaice_calc_rhs.F |
230 |
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o pkg/exf: some cleaning-up: |
231 |
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- change various "constants" into runtime parameters |
232 |
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- cleaned-up Large&Yeager04 routine which should eventually |
233 |
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replace exf_bulkformulae.F (changed names of S/R and CPP) |
234 |
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and merged various ALLOW_ATM_WIND options |
235 |
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only used with thsice pkg (in thsice_get_exf.F): |
236 |
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- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
237 |
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which are used when useStabilityFct_overIce=TRUE (= the default) |
238 |
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- change default values of ice & snow emissivity and scale downward LW |
239 |
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by ice & snow emissivity. |
240 |
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o pkg/thsice: |
241 |
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fix few little problems, in thsice_calc_thickn.F: |
242 |
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- growth vertically (and not laterally) if iceFrac == iceMaskMax |
243 |
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- melt only laterally if hIce < hThinIce (as the comments say) |
244 |
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and in thsice_extend.F: |
245 |
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- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
246 |
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- start to form ice as soon as the minimum ice-volume is reachable. |
247 |
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update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
248 |
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and cpl_aim+ocn |
249 |
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o pkg/kpp |
250 |
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- move computation of surface related input fields to KPP into a new |
251 |
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subroutine kpp_forcing_surf.F |
252 |
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- remove wrong (within bi,bj loops) EXCH calls. |
253 |
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- little cleaning (add argument myThid in last position, cvs header ...) |
254 |
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- for now, fix conservation problem by exchanging KPPviscAz (may not |
255 |
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be the best fix) |
256 |
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o pkg/seaice |
257 |
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- check for inconsistent evp parameter/cpp-flag combination |
258 |
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- remove leftover errIO flat for obsolete name list error handling |
259 |
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o OpenAD |
260 |
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- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
261 |
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|
262 |
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checkpoint59a |
263 |
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o pkg/seaice: some parameter clarifications and a little bit of clean up |
264 |
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o pkg/thsice: rename run-time parameters: |
265 |
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himin -> hIceMin |
266 |
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himin0 -> hThinIce |
267 |
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hihig -> hThickIce |
268 |
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i0 -> i0swFrac |
269 |
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transCoef -> bMeltCoef |
270 |
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frac_energy -> fracMelting |
271 |
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add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
272 |
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with default values (for now) that do not change the results. |
273 |
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remove old version of thsice vars advection in pkg/seaice. |
274 |
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o in FFIELDS.h: |
275 |
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- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
276 |
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- make pLoad & sIceLoad always available (but still only used if |
277 |
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ATMOSPHERIC_LOADING is #define). |
278 |
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o pkg/kpp: replaced _KPP_RL with _RL |
279 |
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o bug fixes for vertical diffusivity computations when both KPP and |
280 |
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3D diffusivity arrays are used. |
281 |
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o pkg/seaice: fix bug in evp solver, while doing that |
282 |
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- change (improve?) discretization of stress computations for both |
283 |
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cgrid-lsr and evp solver |
284 |
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- add a new routine to compute strain rates |
285 |
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- the above changes lab_sea results |
286 |
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- add no slip conditions for evp solver (off by default), lsr-version |
287 |
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may follow |
288 |
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- fix exchange for shear at Z-points (does not change lab_sea) |
289 |
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- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
290 |
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(to force the user to pick a time step since there is not "safe" way |
291 |
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of choosing it) |
292 |
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- add principal stress diagnostics |
293 |
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- rearrange fields for evp a little to avoid having to call a: too many |
294 |
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exchanges and b: exchanges for stress trensor components which we do |
295 |
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not have. |
296 |
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- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
297 |
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of evp, complete rewrite for lsr case (latter is does not yet work |
298 |
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in all cases) |
299 |
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o pkg/kpp: add code to have mixing in shelf ice caverns |
300 |
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- add myThid to all kpp routines (long overdue) |
301 |
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|
302 |
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checkpoint59 |
303 |
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o pkg/exf: |
304 |
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- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
305 |
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ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
306 |
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- move exf header files from lower_case.h to UPPER_CASE.h ; |
307 |
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add missing cvs Header & Name |
308 |
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- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
309 |
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- add namelist param. selectStressGridPosition, exf_monFreq |
310 |
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- retire many _CLIM routines, and remove data.exf_clim |
311 |
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+ params moved to data.exf |
312 |
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+ climsst, climsss now handled by exf_set_gen, i.e. |
313 |
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climss?period=0 refers to constant field, |
314 |
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climss?period=-12 to monthly forcing |
315 |
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- split up namelists in data.exf |
316 |
|
o pkg/seaice: |
317 |
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- remove seaice_exch and seaice_exch_uv |
318 |
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- remove superfluous exchange of theta |
319 |
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- add myThid to seaice_budget_ocean/ice |
320 |
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- add new interface for atmospheric wind forcing (C-grid only) |
321 |
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+ new routine |
322 |
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+ two new field (taux, tauy for stress over ice) |
323 |
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+ removed one global field (DAIRN) for C-grid case only |
324 |
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o pkg/thsise |
325 |
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- 2nd set of modifs for thsice adjoint in conjunction with exf |
326 |
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o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
327 |
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|
328 |
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checkpoint58y_post |
329 |
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o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
330 |
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vertical diffusivity, similar to that in MOM4; turned on using |
331 |
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#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
332 |
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diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
333 |
|
o Added capability for 3D specification of background vertical diffusion |
334 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
335 |
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in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
336 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
337 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
338 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
339 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
340 |
|
but: - conserving Mass, Heat & Salt. |
341 |
|
- better when using non-linear advection scheme (not yet fully tested) |
342 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
343 |
|
|
344 |
|
checkpoint58x_post |
345 |
|
o IO option for global-file compact format: |
346 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
347 |
|
- add I/O capability (pkg/mdsio). |
348 |
|
- adapt utils/matlab/rdmds.m to read this format. |
349 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
350 |
|
o shelfice: add a few diagnostics |
351 |
|
|
352 |
|
checkpoint58w_post |
353 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
354 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
355 |
|
(and replace horiVertRatio in NH code). |
356 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
357 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
358 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
359 |
|
directly to drive seaice model (C-grid only) |
360 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
361 |
|
- reintroduce computation of wind from stress, |
362 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
363 |
|
mass points to avoid tau = 0 |
364 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
365 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
366 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
367 |
|
(tested on all testreport mnc output files). |
368 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
369 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
370 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
371 |
|
to all packages |
372 |
|
|
373 |
|
checkpoint58v_post |
374 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
375 |
|
useDynP_inEos_Zc tested. |
376 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
377 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
378 |
|
and portions thereof. See read_cs.txt for description and examples. |
379 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
380 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
381 |
|
following the great-circle arc between those 2 points. |
382 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
383 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
384 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
385 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
386 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
387 |
|
- still needs work (not working with some options ; efficiency to improve) |
388 |
|
and serious testing. |
389 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
390 |
|
advect_xy & advect_xz, respectively. |
391 |
|
|
392 |
|
checkpoint58u_post |
393 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
394 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
395 |
|
o testreport: add option "-skipdir" to skip some test. |
396 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
397 |
|
momentum calculation. |
398 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
399 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
400 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
401 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
402 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
403 |
|
Linear Free surface |
404 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
405 |
|
o pkg/thsice: fix reading mnc-pickups |
406 |
|
|
407 |
|
checkpoint58t_post |
408 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
409 |
|
o pkg/mdsio: |
410 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
411 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
412 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
413 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
414 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
415 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
416 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
417 |
|
informations (variable names, time ...) to meta files. |
418 |
|
- modify rdmds.m to give back the meta file content. |
419 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
420 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
421 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
422 |
|
diagnostic pointer. |
423 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
424 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
425 |
|
o fix multi-category seaice: |
426 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
427 |
|
SEAICE_MULTICATEGORY |
428 |
|
- fix short wave heat flux |
429 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
430 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
431 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
432 |
|
o Initial check-in of lab_sea adjoint |
433 |
|
(very similar to natl_box_adjoint/code_seaice) |
434 |
|
* used C-grid and EVP solver |
435 |
|
* used KPP, GM/Redi |
436 |
|
* uses inAdExact=.TRUE. |
437 |
|
* gradient checks fail for both ADM and TLM |
438 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
439 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
440 |
|
issue is related to forward mismatch between g77 an ifort |
441 |
|
o pkg/seaice: overhaul of thermodynamics |
442 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
443 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
444 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
445 |
|
make them 2D (FICE/QNETO/ ...) |
446 |
|
- remove FO (it is the same as QNETO) |
447 |
|
- introduce a few local fields to avoid modifying external fields such |
448 |
|
as atemp, etc. |
449 |
|
|
450 |
|
checkpoint58s_post |
451 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
452 |
|
changed exf_set_gen.F so that |
453 |
|
genperiod=0 means input file is one time-constant field and |
454 |
|
genperiod=-12 means input file contains 12 monthly means |
455 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
456 |
|
this affects truncation error ; generate new output file for exp. which |
457 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
458 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
459 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
460 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
461 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
462 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
463 |
|
o start implementation of deep-atmosphere and anelastic formulation |
464 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
465 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
466 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
467 |
|
o profiles: fix for multithreaded case |
468 |
|
|
469 |
|
o diagnostics: rename few diags: |
470 |
|
s/'PRESSURE'/'RCENTER '/g |
471 |
|
s/'TICE '/'oceFreez'/g |
472 |
|
s/'TAUX '/'oceTAUX '/g |
473 |
|
s/'TAUY '/'oceTAUY '/g |
474 |
|
s/'SWFLUX '/'oceQsw '/g |
475 |
|
s/DIFx/DFxE/g |
476 |
|
s/DIFy/DFyE/g |
477 |
|
and add few ocean-forcing diagnostics: |
478 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
479 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
480 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
481 |
|
as actual snow thickness. It now refers everywhere to effective snow |
482 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
483 |
|
|
484 |
|
checkpoint58r_post |
485 |
|
o modifications to pkg/seaice/growth.F, which change results of |
486 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
487 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
488 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
489 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
490 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
491 |
|
both are turned off by default and do no change any results |
492 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
493 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
494 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
495 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
496 |
|
in natl_box (affects results @ truncation level: update output.txt) |
497 |
|
o multi-threading and IO: |
498 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
499 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
500 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
501 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
502 |
|
affects the results (but none of the verification test uses this scheme). |
503 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
504 |
|
(will certainly be subject to changes) |
505 |
|
o ctrl: adding new control variables: |
506 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
507 |
|
|
508 |
|
checkpoint58q_post |
509 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
510 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
511 |
|
high_res_cube configuration by 4% on Columbia. |
512 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
513 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
514 |
|
dynamical allocation (seems to work in multi-threaded). |
515 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
516 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
517 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
518 |
|
|
519 |
|
checkpoint58p_post |
520 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
521 |
|
o shelfice: |
522 |
|
- fix a sign error so that no slip at shelfice interface works |
523 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
524 |
|
not mean, that the results are correct, but at least they are numerically |
525 |
|
stable |
526 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
527 |
|
o added adjoint exch routined for all exch*3d* routines |
528 |
|
and updated flow directives |
529 |
|
|
530 |
|
checkpoint58o_post |
531 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
532 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
533 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
534 |
|
and clean-up reading/writing of pickup files. |
535 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
536 |
|
o simplify EXCH interface: |
537 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
538 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
539 |
|
o added the regrid package |
540 |
|
o shelfice: |
541 |
|
- add a simple boundary layer scheme to reduce noise |
542 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
543 |
|
|
544 |
|
checkpoint58n_post |
545 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
546 |
|
local variable (not in common block). |
547 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
548 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
549 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
550 |
|
to work with SingleCpuIO. |
551 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
552 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
553 |
|
o multi-threading and IO: |
554 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
555 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
556 |
|
- barrier before and after reading. |
557 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
558 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
559 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
560 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
561 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
562 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
563 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
564 |
|
|
565 |
|
checkpoint58m_post |
566 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
567 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
568 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
569 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
570 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
571 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
572 |
|
add MITgcm_tutorials (= code + all the tutorials) |
573 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
574 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
575 |
|
o profiles: adding ptracer and ssh |
576 |
|
o testreport: change multi-test output-file name |
577 |
|
(from output.txt.{name} to output.{name}.txt) |
578 |
|
o profiles: now ok for mutli-tiles case |
579 |
|
o seaice: add 4 parameters for different advection schemes for area, |
580 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
581 |
|
is the standard parameter SEAICEadvScheme |
582 |
|
o calc_gw: |
583 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
584 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
585 |
|
of tutorial_plume_on_slope. |
586 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
587 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
588 |
|
update rotating_tank results, but not plume_on_slope (affected at |
589 |
|
truncation level, 11 digits). |
590 |
|
|
591 |
|
checkpoint58l_post |
592 |
|
o calc_gw: |
593 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
594 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
595 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
596 |
|
o commit code to make SST/SSS weights spatially variable |
597 |
|
(based on either variable in-situ or variable initial T/S weights) |
598 |
|
o pkg/ecco: |
599 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
600 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
601 |
|
* cost_averagesflags now returns year indices in addition to day, month |
602 |
|
* sflux balance is performed on annual basis |
603 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
604 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
605 |
|
including separate counting and multipliers |
606 |
|
o pkg/rbcs |
607 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
608 |
|
|
609 |
|
checkpoint58k_post |
610 |
|
o testreport: |
611 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
612 |
|
& running in input) |
613 |
|
- run in dir run (if it exists), in build otherwise. |
614 |
|
- call prepare_run (if input/prepare_run exists) |
615 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
616 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
617 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
618 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
619 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
620 |
|
o pkg/exf/exf_check_range.F |
621 |
|
- add tile index to diagnostics and move stop statement to the very |
622 |
|
end of the routine. |
623 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
624 |
|
define title of isomorphic variables according to the current config. |
625 |
|
o pkg/thsice with pkg/seaice dynamics: |
626 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
627 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
628 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
629 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
630 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
631 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
632 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
633 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
634 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
635 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
636 |
|
o tracer advection: |
637 |
|
- clean-up and simplify calc_common_factors.F |
638 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
639 |
|
advection subroutine (but still not used within DST advection S/R) |
640 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
641 |
|
|
642 |
|
checkpoint58j_post |
643 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
644 |
|
from file (collects calls previously in FORWARD_STEP) |
645 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
646 |
|
o adjoint store dir. adjusted accordingly |
647 |
|
o genmake2 |
648 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
649 |
|
|
650 |
|
checkpoint58i_post |
651 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
652 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
653 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
654 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
655 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
656 |
|
on CS-grid: no longer loosing mass. |
657 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
658 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
659 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
660 |
|
- Set to false in order to start EVP solver with |
661 |
|
non-EVP pickup files when using SEAICEuseEVP |
662 |
|
- fix sign error in diffusion in seaice_calc_rhs |
663 |
|
|
664 |
|
checkpoint58h_post |
665 |
|
* Modifications for bottom topography control |
666 |
|
o replace hFacC by _hFacC at various places |
667 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
668 |
|
o add non-self-adjoint cg2d_nsa |
669 |
|
o update autodiff support routines |
670 |
|
o re-initialise hfac after ctrl_depth_ini |
671 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
672 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
673 |
|
|
674 |
|
checkpoint58g_post |
675 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
676 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
677 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
678 |
|
o pkg/ggl90: |
679 |
|
- add parameter (minimum surface kinetic energy) |
680 |
|
- fix bug (avoiding division by zero) |
681 |
|
o couple pkg/thsice to pkg/seaice: |
682 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
683 |
|
- only muliDimAdection scheme work with seaice/thsice |
684 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
685 |
|
- does not break the verification experiments, but does not give the |
686 |
|
desired results either |
687 |
|
o pkg/seaice |
688 |
|
- make (default) second order advection a bit less confusing? |
689 |
|
|
690 |
|
checkpoint58f_post |
691 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
692 |
|
to pkg/seaice): |
693 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
694 |
|
- add an additional formal parameter to thsice_solve4temp |
695 |
|
o pkg/exf: |
696 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
697 |
|
- correct Stefan-Boltzmann constant |
698 |
|
- new parameter for longwave surface emittance |
699 |
|
- separate some stuff from exf_bulkformulae into new routines |
700 |
|
exf_radiation, exf_wind |
701 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
702 |
|
and snow, evaporation parameters over ice |
703 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
704 |
|
either wind from stress or stress from wind |
705 |
|
o pkg/thSIce: |
706 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
707 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
708 |
|
and THSICE_CALC_THICKN |
709 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
710 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
711 |
|
to make debugging easier. |
712 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
713 |
|
o pkg/bulk_force: |
714 |
|
- clean-up comments and parameters ; |
715 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
716 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
717 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
718 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
719 |
|
testreport accordingly |
720 |
|
|
721 |
|
checkpoint58e_post |
722 |
|
o SEAICE_CGRID adjoint done |
723 |
|
o R_STAR adjoint implemented. |
724 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
725 |
|
* need to sort out init. of h0facc, etc. |
726 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
727 |
|
to be able to use it in pure forward. |
728 |
|
|
729 |
|
checkpoint58d_post |
730 |
|
o upgrade simple test-experiment to tutorial example: |
731 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
732 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
733 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
734 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
735 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
736 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
737 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
738 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
739 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
740 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
741 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
742 |
|
o correct a sign problem in cost_scat.F |
743 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
744 |
|
with larger stencil |
745 |
|
o thsice adjoint: start |
746 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
747 |
|
completeness |
748 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
749 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
750 |
|
o ptracers adjoint: |
751 |
|
* avoid extensive recomputatations |
752 |
|
* fix missing re-init. of gptr (missed by TAF) |
753 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
754 |
|
me to turn off the excessive output to STDOUT that this package produces |
755 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
756 |
|
and add those terms in Vector-Invariant formulation. |
757 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
758 |
|
if the control period (xx_hfluxperiod etc) is 0 |
759 |
|
o in profiles pkg, clean routines and fix details |
760 |
|
o in ecco pkg, reading ssh data: |
761 |
|
fix problem in case the model does not start at iter0=0 |
762 |
|
o fix mnc-pickup/restart for ptracers |
763 |
|
o new package prifiles: |
764 |
|
code to compute profile-based cost by Gael Forget |
765 |
|
(modifs in ecco, ctrl, autodiff) |
766 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
767 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
768 |
|
|
769 |
|
checkpoint58c_post |
770 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
771 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
772 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
773 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
774 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
775 |
|
with SEAICE_CGRID defined. |
776 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
777 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
778 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
779 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
780 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
781 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
782 |
|
o fix bug in quasihydrostatic S/R ; |
783 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
784 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
785 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
786 |
|
o add on/off flag useOffLine for package OFFLINE |
787 |
|
o seaice: |
788 |
|
- modify advection so that it works also on the C-grid |
789 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
790 |
|
problem in multi-tile runs with C-grid |
791 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
792 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
793 |
|
C-grid solver |
794 |
|
- added a few comments to seaice_diffusion.F |
795 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
796 |
|
are now exclusive) |
797 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
798 |
|
required re-ordering the code a little: |
799 |
|
+ make DAIRN global variable (defined in SEAICE) |
800 |
|
+ move computation of the viscosities eta and zeta into a new separate |
801 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
802 |
|
|
803 |
|
checkpoint58b_post |
804 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
805 |
|
update output.txt of exp. aim.5l_cs.thSI |
806 |
|
o various mnc cleanups and improvements: |
807 |
|
+ shrink lookup tables by factor of ~4 |
808 |
|
+ better error reporting when running out of lookup space |
809 |
|
+ able to handle longer path/file names (up to 500 chars) |
810 |
|
o adjoint: |
811 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
812 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
813 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
814 |
|
(allow to differentiate between forcing components using new integer flags: |
815 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
816 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
817 |
|
o ecco |
818 |
|
- enable trend removal from SSH anomaly obs. |
819 |
|
o adjoint |
820 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
821 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
822 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
823 |
|
(NLFS seems broken sometimes after I checked it in) |
824 |
|
o seaice: |
825 |
|
- add c-grid version of the dynamic solver: |
826 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
827 |
|
and ostres |
828 |
|
+ put a few fields that were local to dynsolver into global common |
829 |
|
blocks, so that I can move the computation of stresses etc into |
830 |
|
seaice_lsr (saves coding but may break the adjoint). |
831 |
|
- replace more hardwired parameters by runtime parameters |
832 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
833 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
834 |
|
if this works properly), eventually this should replace the clipping |
835 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
836 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
837 |
|
include it only where its needed |
838 |
|
o move balancing of fluxes before the call of external_forcing_surf |
839 |
|
o seaice: |
840 |
|
- correct units of turning angles (now they are really in degrees) |
841 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
842 |
|
- initialize GWATX/Y in seaice_init |
843 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
844 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
845 |
|
o seaice: add runtime flags for turning angles (default to zero) |
846 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
847 |
|
and trend from exf forcing and ctrl control adjustments |
848 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
849 |
|
(since checkpoint57x_post) |
850 |
|
o change the default rotation period to 86164.s = the Earth rotation |
851 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
852 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
853 |
|
o seaice advection: add code for choosing between the default (2nd order |
854 |
|
central differences) and multiDim advection schemes provided by |
855 |
|
pkg/generic_advdiff |
856 |
|
o seaice: |
857 |
|
- removed all references to SEAICE_GRID.h fields from |
858 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
859 |
|
(cubed-sphere configuration will change a little) |
860 |
|
- grid computations in seaice_init are obsolete now. |
861 |
|
- cleaned up code a little so that is easier to read (hopefully). |
862 |
|
- added new (better?) discretizations of default advection and diffusion |
863 |
|
(turn on with SEAICEuseFluxForm) |
864 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
865 |
|
|
866 |
|
checkpoint58a_post |
867 |
|
o seaice: |
868 |
|
- bug fix in advect.F |
869 |
|
o shelfice: |
870 |
|
- separate shelfice load anomaly from pload (breaks with time |
871 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
872 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
873 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
874 |
|
done offline. A good approximation of the pressure load anomaly is |
875 |
|
necessary to avoid large initial adjustment processes underneath |
876 |
|
deep-reaching shelfice. |
877 |
|
- small fix in ISOMIP shelfice_thermodynamics |
878 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
879 |
|
now the default |
880 |
|
- give a few constants more intuitive names |
881 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
882 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
883 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
884 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
885 |
|
STDOUT. |
886 |
|
o fix bug (typo) in obcs_apply_eta.F |
887 |
|
o add a new package shelfice which enables us to model the circulation |
888 |
|
underneath shelf-ice with draughts of hundreds of meters. |
889 |
|
- works |
890 |
|
- to do: + include improved thermodynamics |
891 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
892 |
|
instead of new field kTopC |
893 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
894 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
895 |
|
and ini_mask_etc.F? |
896 |
|
+ adjust vertical mixing schemes? |
897 |
|
o seaice pkg: |
898 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
899 |
|
freezing point of sea water at the surface |
900 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
901 |
|
meridional stresses are now different (and hopefully correct) |
902 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
903 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
904 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
905 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
906 |
|
diagnostics ; define regions by reading a region-mask from a file |
907 |
|
(might add other options later) |
908 |
|
o pkg/bulk_force: |
909 |
|
- add option and parameters to use AIM surface-flux formulae. |
910 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
911 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
912 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
913 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
914 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
915 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
916 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
917 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
918 |
|
|
919 |
|
checkpoint58 |
920 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
921 |
|
tools can be compiled (as determined by genmake2) will turn on the |
922 |
|
embed_files package which then embeds the entire MITgcm source code |
923 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
924 |
|
- requested by CNH but off by default |
925 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
926 |
|
- only writes the output when useEMBEDSRC in eedata is true |
927 |
|
o clean up 3-dim. relaxation codes: |
928 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
929 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
930 |
|
* Thanks to Tom Haine for testing! |
931 |
|
|
932 |
|
checkpoint57z_post |
933 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
934 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
935 |
|
o fix the pickup behavior for obcs in combination with ptracers |
936 |
|
o fix a bug in ptracers_external_fields_load |
937 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
938 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
939 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
940 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
941 |
|
and update lab_sea output.txt file. |
942 |
|
o completing 3-dim. relaxation code: additional term |
943 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
944 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
945 |
|
* At compile time, in "EXF_OPTIONS.h" set |
946 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
947 |
|
#define ALLOW_CLIMSALT_RELAXATION |
948 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
949 |
|
tauThetaClimRelax3Dim = 15552000.0, |
950 |
|
tauSaltClimRelax3Dim = 15552000.0, |
951 |
|
* 3 cases: |
952 |
|
1) Use a constant-in-time 3-dim. field |
953 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
954 |
|
3) Real-time relax. to time-evolving prescribed field |
955 |
|
o Adding Laplacian-type smoothness constraint on |
956 |
|
initial and boundary (forcing) controls (ic, bc) |
957 |
|
* enable at compile-time via |
958 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
959 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
960 |
|
* Absolute scale somewhat unclear so far |
961 |
|
* no area weighting was included since no other cost term does so far |
962 |
|
|
963 |
|
checkpoint57y_post |
964 |
|
First step for a NLFS adjoint |
965 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
966 |
|
o new init. routines for calc_r_star, calc_surf_dr |
967 |
|
o still need to deal with ini_masks_etc |
968 |
|
o testreport seemed happy |
969 |
|
checkpoint57y_pre |
970 |
|
|
971 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
972 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
973 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
974 |
|
o cfc fixes for final year of integration |
975 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
976 |
|
be in GCHEM_OPTIONS). |
977 |
|
|
978 |
|
checkpoint57x_post |
979 |
|
o fix testreport Pb in multiple test experiment. |
980 |
|
o cleanup our namelist syntax in verification: |
981 |
|
- make it more F95 standards compliant (some work still needed) |
982 |
|
- allows the vast majority of our tests to work with gfortran |
983 |
|
o Non-Hydrostatic: |
984 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
985 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
986 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
987 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
988 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
989 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
990 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
991 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
992 |
|
o remove some unused variables (reduces number of compiler warnings) |
993 |
|
o adjoint |
994 |
|
* Disable useVariableViscosity for adjoint for time being |
995 |
|
(there are a number of extensive recomputations) |
996 |
|
* Initialize certain variables needed for adjoint |
997 |
|
|
998 |
|
checkpoint57w_post |
999 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
1000 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
1001 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
1002 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
1003 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
1004 |
|
o tracer advection scheme: |
1005 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
1006 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
1007 |
|
was not very convenient). |
1008 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
1009 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
1010 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
1011 |
|
and sRef for convenience, handy, when you want to initialize |
1012 |
|
ptracers in a large domain with a constant non-zero value. Also, |
1013 |
|
untangle ptracers_init.F a little. |
1014 |
|
|
1015 |
|
checkpoint57v_post |
1016 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
1017 |
|
o remove all the files from the cfc_offline test since they are now |
1018 |
|
incorporated into tutorial_cfc_offline which has been producing |
1019 |
|
identical results for a few days of testing |
1020 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
1021 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
1022 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
1023 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
1024 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
1025 |
|
o vorticity & strain are now computed without masking, to account for |
1026 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
1027 |
|
anyway later on, before computing advection/coriolis terms. |
1028 |
|
o modify exp4 to test new obcs support for reading from external files |
1029 |
|
and for passive tracers |
1030 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
1031 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
1032 |
|
file). |
1033 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
1034 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
1035 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
1036 |
|
to be proportional to enstrophy dissipation length. Thus, |
1037 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
1038 |
|
This is now consistent with Smagorinsky and with the manual. |
1039 |
|
|
1040 |
|
checkpoint57u_post |
1041 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
1042 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
1043 |
|
OB-values from file; this is not different from the way theta and salinity |
1044 |
|
are treated |
1045 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
1046 |
|
will stop if you use pTracers and Orlanski at the same time. |
1047 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
1048 |
|
boundary values are overwritten with values from files for which there |
1049 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
1050 |
|
it possible to use different OBs at different ends of the domain (as |
1051 |
|
with EXF) |
1052 |
|
o reduce number of exch calls in shap_filt (s2). |
1053 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
1054 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
1055 |
|
|
1056 |
|
checkpoint57t_post |
1057 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
1058 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
1059 |
|
same truncation, independent of the face number: affects affects several |
1060 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
1061 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
1062 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
1063 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
1064 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
1065 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
1066 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
1067 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
1068 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
1069 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
1070 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
1071 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
1072 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
1073 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
1074 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
1075 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
1076 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
1077 |
|
Many new viscosity diagnostics available. |
1078 |
|
|
1079 |
|
checkpoint57s_post |
1080 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
1081 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
1082 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
1083 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
1084 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
1085 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
1086 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
1087 |
|
ViscAhStrain and viscAhTension are now retired. |
1088 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
1089 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
1090 |
|
that it finds in the *current* directory when searching for files. |
1091 |
|
Soft-links found in any other source directories will still work as |
1092 |
|
they did before. |
1093 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
1094 |
|
a C routine to unlimit the stack size |
1095 |
|
o mnc-ify pkg/aim snapshot vars |
1096 |
|
o mnc-ify pkg/land as requested by Daniel |
1097 |
|
o various changes to mnc including: |
1098 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
1099 |
|
- output can now be grouped so that all files within a group |
1100 |
|
change the ITER portion of their names in lock-step together |
1101 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
1102 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
1103 |
|
- writing works for all verification test cases w/ g77 on Linux |
1104 |
|
|
1105 |
|
checkpoint57r_post |
1106 |
|
o make MNC variable initialization happen earlier |
1107 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
1108 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
1109 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
1110 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
1111 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
1112 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
1113 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
1114 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
1115 |
|
o add time-dependent SST, SSS control |
1116 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
1117 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
1118 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
1119 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
1120 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
1121 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
1122 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
1123 |
|
(see README file) |
1124 |
|
|
1125 |
|
checkpoint57q_post |
1126 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
1127 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
1128 |
|
- bug was reported by Jean-Michel and Ian Fenty |
1129 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
1130 |
|
update exp. cpl_aim+ocn output. |
1131 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
1132 |
|
Needed for high-res. runs with large global files |
1133 |
|
to be able to limit tapelev size |
1134 |
|
o Changed some tests for adjoint: |
1135 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
1136 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
1137 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
1138 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
1139 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
1140 |
|
* converts, compiles and runs successfully; |
1141 |
|
|
1142 |
|
checkpoint57p_post |
1143 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
1144 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
1145 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
1146 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
1147 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
1148 |
|
(was already the case for dissipation with mom_vecinv, |
1149 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
1150 |
|
This will allow to put dissipation out-off the AB time-stepping. |
1151 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
1152 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
1153 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
1154 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
1155 |
|
|
1156 |
|
checkpoint57o_post |
1157 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
1158 |
|
(2) its ready to be documented during the 20050801 DocFest |
1159 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
1160 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
1161 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
1162 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
1163 |
|
(worth another tag) |
1164 |
|
|
1165 |
|
checkpoint57n_post |
1166 |
|
o adding precip control xx_precip 32 |
1167 |
|
o adding swflux control xx_swflux 33 |
1168 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
1169 |
|
o Implementing partitioning in time-mean and variable adjustment |
1170 |
|
for atmos. state. |
1171 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
1172 |
|
o in natl_box_adjoint: |
1173 |
|
* updated exp 1 to 10 |
1174 |
|
(but does not have time-mean vs. variable split results yet) |
1175 |
|
o updated global1x1/*_seaice_adj/ |
1176 |
|
to incorporate latest changes |
1177 |
|
o enable useSingleCpuIO for mdsio vector routines |
1178 |
|
(applies in particular to tapelev I/O) |
1179 |
|
o removed inefficient K-loop in all active_file*control*.F |
1180 |
|
|
1181 |
|
checkpoint57m_post |
1182 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
1183 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
1184 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
1185 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
1186 |
|
|
1187 |
|
checkpoint57l_post |
1188 |
|
tag before updating tutorials (pre-release-2) |
1189 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
1190 |
|
for output and interpolation of input fields onto model grid) |
1191 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
1192 |
|
Affects results of exp. rotating_tank ; update output.txt. |
1193 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
1194 |
|
and taking the square quantity and/or using a fraction-weight field. |
1195 |
|
o fix aim_diagnostics_init.F mate numbers. |
1196 |
|
o add mnc output capability to diagnostics/diagstat and update |
1197 |
|
our cvsignore files for the ACSII output generated |
1198 |
|
|
1199 |
|
checkpoint57k_post |
1200 |
|
o lab_sea now uses diagnostics package and provides a suite of |
1201 |
|
new EXF diagnostics output. |
1202 |
|
|
1203 |
|
checkpoint57j_post |
1204 |
|
o exf |
1205 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
1206 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
1207 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
1208 |
|
* extended diagnostics output |
1209 |
|
- now includes all EXF variables |
1210 |
|
- hs, hl moved to common block |
1211 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
1212 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
1213 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
1214 |
|
* updated verif. lab_sea, global_with_exf |
1215 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
1216 |
|
to ensure that diagnostics sees a true EXFqnet |
1217 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
1218 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
1219 |
|
several times with different frequencies. |
1220 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
1221 |
|
- the monitor--MNC output needs work |
1222 |
|
- many attributes need to be added (most are currently blank) |
1223 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
1224 |
|
- many attributes need to be added (most are currently blank) |
1225 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
1226 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
1227 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
1228 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
1229 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
1230 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
1231 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
1232 |
|
|
1233 |
|
checkpoint57i_post |
1234 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
1235 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
1236 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
1237 |
|
add 1rst Order upwind vertical Shear. |
1238 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
1239 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
1240 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
1241 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
1242 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
1243 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
1244 |
|
some "_d 0", etc. no effect. |
1245 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
1246 |
|
separate 'iter' variable for iteration count |
1247 |
|
o pkg/diagnostics: |
1248 |
|
add new capability: output of Global/Regional & per-level statistics ; |
1249 |
|
tested against monitor output (including land & thSIce) on various exp. |
1250 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
1251 |
|
|
1252 |
|
checkpoint57h_done |
1253 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
1254 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
1255 |
|
|
1256 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
1257 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
1258 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
1259 |
|
and rename it: DIFFERENT_MULTIPLE |
1260 |
|
|
1261 |
|
checkpoint57h_post |
1262 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
1263 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
1264 |
|
of Nb of iterations). This requires to change data.diagnostics. |
1265 |
|
checkpoint57h_pre |
1266 |
|
|
1267 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
1268 |
|
and mnc_outdir_num are false |
1269 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
1270 |
|
per-file basis, the file precision [default behavior is unchanged] |
1271 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
1272 |
|
depth based on a temperature/density criterion |
1273 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
1274 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
1275 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
1276 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
1277 |
|
not mnc -- this mistake was found by JMC and is now corrected |
1278 |
|
|
1279 |
|
checkpoint57g_post |
1280 |
|
o add Adams-Bashforth 3rd Order time stepping: |
1281 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
1282 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
1283 |
|
checkpoint57g_pre |
1284 |
|
|
1285 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
1286 |
|
(default remains spatially uniform constant based on tau) |
1287 |
|
o added new control variables |
1288 |
|
* init. uVel, vVel, etanN |
1289 |
|
* lambda[Theta,Salt]ClimRelax |
1290 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
1291 |
|
(suggested by G. Forget) |
1292 |
|
|
1293 |
|
checkpoint57f_post |
1294 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
1295 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
1296 |
|
account for baseTime shift |
1297 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
1298 |
|
checkpoint57f_pre |
1299 |
|
|
1300 |
|
o mnc-ifying the seaice package |
1301 |
|
o introduced an alternative length scale calculation for use in the limiting |
1302 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
1303 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
1304 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
1305 |
|
as well as grad(vort3). Made it compatible with both approximate form |
1306 |
|
for the cubed sphere and full form of these gradients. Added flag |
1307 |
|
useFullLeith to select between approximate and full form. |
1308 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
1309 |
|
update output.txt of exp. fizhi-gridalt-hs |
1310 |
|
o change port_rand funtion to allow to set the seed. |
1311 |
|
o fix obscure MNC bug involving conversion between reals and integers |
1312 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
1313 |
|
new version is now more standards-compliant |
1314 |
|
o adjoint-related modifications |
1315 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
1316 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
1317 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
1318 |
|
|
1319 |
|
checkpoint57e_post |
1320 |
|
o Adding eddy stress controls a la Ferreira et al. |
1321 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
1322 |
|
|
1323 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
1324 |
|
update output.txt of exp. fizhi-gridalt-hs |
1325 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
1326 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
1327 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
1328 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
1329 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
1330 |
|
months and years. Requires pkg/cal. |
1331 |
|
o diagnostics: add pickup functionality |
1332 |
|
- off by default for backwards compatibility |
1333 |
|
- current version only uses MDSIO -- MNC will be added |
1334 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
1335 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
1336 |
|
|
1337 |
|
checkpoint57d_post |
1338 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
1339 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
1340 |
|
output from the diagnostics package |
1341 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
1342 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
1343 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
1344 |
|
o add coordinate variables to the MNC output from the diagnostics package |
1345 |
|
o change MNC-flags default value: true when useMNC=TRUE |
1346 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
1347 |
|
the ability (off by default) to read the grid information using MNC |
1348 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
1349 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
1350 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
1351 |
|
at the end). |
1352 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
1353 |
|
new test for AIM with thSIce + slab-ocean |
1354 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
1355 |
|
o move state variable diagnostics to the beginning of the time step ; |
1356 |
|
(note: still needs some work specially for snap-shot diagnostics) |
1357 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
1358 |
|
|
1359 |
|
checkpoint57c_post |
1360 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
1361 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
1362 |
|
checkpoint57c_pre |
1363 |
|
|
1364 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
1365 |
|
update output.txt of exp. global_ocean.90x40x15 |
1366 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
1367 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
1368 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
1369 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
1370 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
1371 |
|
o improvements for the MNC output from DIAGNOSTICS: |
1372 |
|
- correct handling of the unlimitied dimension |
1373 |
|
- all dims now have associated coordinate variables |
1374 |
|
- variables located at U, V, and Corner ("Z") points are now written |
1375 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
1376 |
|
*all* data points are output |
1377 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
1378 |
|
o added pkg/seaice/seaice_monitor.F |
1379 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
1380 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
1381 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
1382 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
1383 |
|
spurious negative numbers for precipitation and humidity. Will cause |
1384 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
1385 |
|
o pkg/ctrl/ |
1386 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
1387 |
|
May be enabled via doPackDiag |
1388 |
|
* introduce z-scaling of |
1389 |
|
+ gradient (doZscalePack) and |
1390 |
|
+ control (doZscaleUnpack) |
1391 |
|
o pkg/mdsio/ |
1392 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
1393 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
1394 |
|
|
1395 |
|
checkpoint57b_post |
1396 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
1397 |
|
o fix MNC coordinate variables so that they now contain per-face index |
1398 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
1399 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
1400 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
1401 |
|
o Implement instantaneous output within pkg diagnostics: |
1402 |
|
setting a negative frequency in data.diagnostics produces |
1403 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
1404 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
1405 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
1406 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
1407 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
1408 |
|
becomes the coordinate variable for the 'T' dimension |
1409 |
|
o add CF-style coordinate variables to MNC |
1410 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
1411 |
|
missing along the T axis but otherwise it works! |
1412 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
1413 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
1414 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
1415 |
|
this is based directly on what the model compute, so that the content of |
1416 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
1417 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
1418 |
|
o clean up build options files for SunOS, in particular |
1419 |
|
- remove -traditional from xmakedepend |
1420 |
|
- change -xarch=v9 to -xarch=native for f77 |
1421 |
|
- restore use of make (not gmake) |
1422 |
|
- add CC=gcc if using g77 |
1423 |
|
o changes per discussion of AM, JMC, & EH3 today: |
1424 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
1425 |
|
creating proper CF-style coordinate variables and in recognition |
1426 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
1427 |
|
the grid files into any of the other NetCDF files |
1428 |
|
- *always* output grid variables with MDSIO (this will eventually be |
1429 |
|
changed) |
1430 |
|
- output MNC grid file if useMNC is true |
1431 |
|
o every instance of _END_MASTER() has been found and replaced with |
1432 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
1433 |
|
preprocessors |
1434 |
|
o re-arrange diagnostics pkg initialisation: |
1435 |
|
- allow each package to extend the available diagnostics list |
1436 |
|
- add some checking and fix small problems (multi-threaded, ...) |
1437 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
1438 |
|
look through the short list of active diag. (instead of the long list) |
1439 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
1440 |
|
|
1441 |
|
checkpoint57a_post |
1442 |
|
o this set of changes restores TAMC compatibility |
1443 |
|
tested for global_ocean.90x40x15 adjoint on trough |
1444 |
|
(what a pain) |
1445 |
|
|
1446 |
|
checkpoint57a_pre |
1447 |
|
o some modifs in tools/build_options for sunos |
1448 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
1449 |
|
|
1450 |
|
checkpoint57 |
1451 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
1452 |
|
- new parameter viscA4W (defaults to viscA4) |
1453 |
|
- affects only non-hydrostatic code |
1454 |
|
- to be done: no-slip lateral boundary conditions |
1455 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
1456 |
|
o implement Implicit Vertical advection for pTracers |
1457 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
1458 |
|
(implemented also for implicit vertical diffusion & advection) |
1459 |
|
o OBCS: extend application of tracer open boundary conditions |
1460 |
|
to a strip beyond the boundary of width Olx/Oly |
1461 |
|
o add call monitor to TAF set of required calls (flow directives) |
1462 |
|
and include in natl_box_adjoint |
1463 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
1464 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
1465 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
1466 |
|
(theta2, salt2 in ecco_cost_weights) |
1467 |
|
|
1468 |
|
checkpoint56c_post |
1469 |
|
o OBCS as control variables |
1470 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
1471 |
|
- remove balance of obcs controls from default |
1472 |
|
- fix index bug nobcs in ctrl_init |
1473 |
|
- fix dummy fields filen in ctrl_pack |
1474 |
|
- add dummy weights for obcs |
1475 |
|
o lsopt: comment out fort.94 output |
1476 |
|
o optim: |
1477 |
|
- remove unnecessary header files |
1478 |
|
- adjusted namelists |
1479 |
|
- add xerbla.F to Makefile |
1480 |
|
o exf: |
1481 |
|
- multiple modifications of exf_check_range |
1482 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
1483 |
|
o mdsio: |
1484 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
1485 |
|
|
1486 |
|
checkpoint56b_post |
1487 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
1488 |
|
is called from DO_THE_MODEL_IO |
1489 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
1490 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
1491 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
1492 |
|
o add another verification experiment that tests both the cfc-pkg and |
1493 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
1494 |
|
reactive tendencies treated inline with regular timestepping |
1495 |
|
o testreport previously did a lousy job of comparing small numbers, so |
1496 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
1497 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
1498 |
|
testreport. |
1499 |
|
o ptracers_monitor: bug fix for MPI |
1500 |
|
|
1501 |
|
checkpoint56a_post |
1502 |
|
o GCHEM: finish reorganizating the package |
1503 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
1504 |
|
(introduces another 3D-array for each passive tracer, but only if |
1505 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
1506 |
|
gchemTendency is not needed because the timestep is done separately) |
1507 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
1508 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
1509 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
1510 |
|
so clear to me how that should be done in a general way. |
1511 |
|
o CFC: improve formatting of output in CFC_ATMOS |
1512 |
|
o PTRACERS: |
1513 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
1514 |
|
that ALL experiments with ptracers enable can be checked. This makes |
1515 |
|
GCHEM_MONITOR obsolete. |
1516 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
1517 |
|
monitorFreq |
1518 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
1519 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
1520 |
|
o exf_check_range: |
1521 |
|
* default changed to .TRUE. |
1522 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
1523 |
|
* STOP in exf_check_range if 'out of range' |
1524 |
|
* range chosen generous to allow for potential extema |
1525 |
|
TBD: a version with stricter range |
1526 |
|
permitted range would be runtime parameters |
1527 |
|
o GMredi: |
1528 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
1529 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
1530 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
1531 |
|
o GCHEM: |
1532 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
1533 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
1534 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
1535 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
1536 |
|
this flag is now only visible within GCHEM-pkg routines. |
1537 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
1538 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
1539 |
|
this, the tracer ID iTracer had to be included into the parameter list |
1540 |
|
of ptracers_forcing |
1541 |
|
- set up forward_step to call gchem_forcing, that will replace |
1542 |
|
gchem_forcing_int in ptracers_forcing |
1543 |
|
- cleaning up |
1544 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
1545 |
|
|
1546 |
|
checkpoint56 |
1547 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
1548 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
1549 |
|
o ECCO-GODAE |
1550 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
1551 |
|
* fully merged and updated from SIO code |
1552 |
|
windstress sign change affects |
1553 |
|
- exf_inscal_[u/v]stress |
1554 |
|
- sign of xx_tau[u/v] adjustments |
1555 |
|
- signs in cost_scat |
1556 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
1557 |
|
* natl_box_adjoint updated and compressed |
1558 |
|
* 2-level checkpoint switch added |
1559 |
|
(tested in EXP. 1 of natl_box_adjoint) |
1560 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
1561 |
|
o SVD |
1562 |
|
* first complete, non-hacked version for SVD calculations |
1563 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
1564 |
|
performed via direct access files admtlm_vector.it???? |
1565 |
|
(via ctrl_[un]pack) |
1566 |
|
* optimcycle is used for ARPACK iteration counter |
1567 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
1568 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
1569 |
|
and add linear transforms where necessary |
1570 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
1571 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
1572 |
|
o mdsio: filename info to both stderr, stdout |
1573 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
1574 |
|
from sign change |
1575 |
|
|
1576 |
|
checkpoint55j_post |
1577 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
1578 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
1579 |
|
o add consistent build directories and .cvsignore files to verification |
1580 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
1581 |
|
o make all subroutines 30 or less characters in length for certain older |
1582 |
|
compilers to work (a thorough search only turns up two routines in |
1583 |
|
pkg/ptracers) |
1584 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
1585 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
1586 |
|
|
1587 |
|
checkpoint55i_post |
1588 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
1589 |
|
3.D if implicit) ; each ptracer uses its own background value. |
1590 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
1591 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
1592 |
|
ITRDA and other clusters without the mpirun "-wd" option |
1593 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
1594 |
|
configuration |
1595 |
|
o give MNC the ability to create additional files rather than |
1596 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
1597 |
|
- the default is just less than 2GB which is a practical limit |
1598 |
|
on many systems |
1599 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
1600 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
1601 |
|
|
1602 |
|
checkpoint55h_post |
1603 |
|
o add verification test "vermix" |
1604 |
|
o remove all the *_ioinc flags and replace with the single global |
1605 |
|
outputTypesInclusive flag |
1606 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
1607 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
1608 |
|
o useMNC moved from data.mnc to data.pkg |
1609 |
|
|
1610 |
|
checkpoint55g_post |
1611 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
1612 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
1613 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
1614 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
1615 |
|
Works well for global_ocean.90x40x15, |
1616 |
|
but recomp. issue remains for carbon |
1617 |
|
o Updating adjoint output for natl_box_adjoint after |
1618 |
|
pkg/ecco has been modified (see taga c55d_post) |
1619 |
|
|
1620 |
|
checkpoint55f_post |
1621 |
|
o rename to timeave_init_fixed |
1622 |
|
|
1623 |
|
checkpoint55e_post |
1624 |
|
o some delicate re-shuffle of store directives to avoid one |
1625 |
|
extra call of do_oceanic_physics |
1626 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
1627 |
|
checkpoint_lev1_directives.h |
1628 |
|
o NB: this may break global_ocean adjoint temporarily, |
1629 |
|
but it is clear how to fix it. Will do later, need this now. |
1630 |
|
|
1631 |
|
checkpoint55d_post |
1632 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
1633 |
|
o ecco_cost_weights is modified to 1x1 runs |
1634 |
|
o modifs to allow observations to be read in as |
1635 |
|
single file or yearly files |
1636 |
|
o enable to read exf forcing fields as either |
1637 |
|
single file or yearly files (flag useExfYearlyFields) |
1638 |
|
checkpoint55d_pre |
1639 |
|
|
1640 |
|
o switch between 2-level and 3-level checkpointing |
1641 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
1642 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
1643 |
|
with the correct (that is, the complete multi-dimensional) set of |
1644 |
|
array indicies |
1645 |
|
- used in mom_vecinv() to write the diagFreq output |
1646 |
|
- tested (demonstrated) in verification/aim.5l_cs |
1647 |
|
o further mnc-ification |
1648 |
|
- add verification/lab_sea to the list with mnc setups |
1649 |
|
- fix undefined mnc v-names in cd_code |
1650 |
|
- add kpp to mnc output (both snapshot and timeave) |
1651 |
|
o non-hydrostatic code |
1652 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
1653 |
|
in calc_gw.F |
1654 |
|
- defaults to viscAh |
1655 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
1656 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
1657 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
1658 |
|
o pkg/cost |
1659 |
|
extend simple cost functions to treat time mean quantities |
1660 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
1661 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
1662 |
|
be 2 times larger than the minimum size the advection scheme requires. |
1663 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
1664 |
|
o GGL90 (Gaspar's TKE mixed layer) |
1665 |
|
- add horizontal diffusion of TKE, requires exchanges in |
1666 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
1667 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
1668 |
|
mixing coefficients are computed from a horizontal average of TKE of |
1669 |
|
6 points or so. I think that diffusion has a little more physical |
1670 |
|
justification. |
1671 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
1672 |
|
was in vain) |
1673 |
|
- mask tke-variable in ggl90_init |
1674 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
1675 |
|
o fix biharmonic diffusion on CS-grid. |
1676 |
|
o more obcs stuff |
1677 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
1678 |
|
for reading boundary values. This routine is called from |
1679 |
|
obcs_prescribe_read |
1680 |
|
- updated obcs_check |
1681 |
|
- changed sponge layer relaxation parameter units for days to seconds |
1682 |
|
- turned off sponge layer by default |
1683 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
1684 |
|
- fixed about 35 bugs in obcs_external_fields_load |
1685 |
|
|
1686 |
|
checkpoint55c_post |
1687 |
|
o obcs stuff |
1688 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
1689 |
|
- re-arranged obcs_calc |
1690 |
|
- moved exf_getobcs to obcs_prescibe_read |
1691 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
1692 |
|
and independent of it (executable can contain all). |
1693 |
|
- updated obcs_check |
1694 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
1695 |
|
These may be necessary only if tangential velocities are |
1696 |
|
prescribed at OB, not sure, needs testing. |
1697 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
1698 |
|
which simplifies the calls and passes the ifc check-bounds test |
1699 |
|
|
1700 |
|
checkpoint55b_post |
1701 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
1702 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
1703 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
1704 |
|
affects advect_cs results (for the wrong reason): update output.txt |
1705 |
|
o use a more standard discretization for biharmonic viscosity ; |
1706 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
1707 |
|
affects results of dome set-up: update output.txt |
1708 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
1709 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
1710 |
|
|
1711 |
|
checkpoint55a_post |
1712 |
|
o merged code to |
1713 |
|
* prescribe/read time-dependent open boundaries |
1714 |
|
(works in conjunction with exf, cal) |
1715 |
|
* sponge layer code for open boundaries |
1716 |
|
* each boundary N/S/E/W now has its own CPP option |
1717 |
|
(healthy for the adjoint) |
1718 |
|
|
1719 |
|
checkpoint55 |
1720 |
|
o up-to-date adjoint of previous breaks |
1721 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
1722 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
1723 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
1724 |
|
- carbon: * remove tr1-related adjoint verification |
1725 |
|
* add ptracer as control variable |
1726 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
1727 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
1728 |
|
|
1729 |
|
checkpoint54f_post |
1730 |
|
o in verification/carbin/ remove experiment related to |
1731 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
1732 |
|
code_ad/ input_ad/ results_ad |
1733 |
|
|
1734 |
|
o add two new packages |
1735 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
1736 |
|
+ subject to optimization (memory) |
1737 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
1738 |
|
+ subject to reordering (many GOTOs in the original code) |
1739 |
|
+ so far opps is called for every (i,j) point, and then operates in |
1740 |
|
the vertical; one may want to reorder the scheme in order operate in |
1741 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
1742 |
|
fields) |
1743 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
1744 |
|
- all verification tests compile and run with linux_ia32_g77 |
1745 |
|
- defaults are compatible with current input files--nothing |
1746 |
|
should change if you were not previously using MNC |
1747 |
|
- MNC output has been added in numerous places (eg. timeave) |
1748 |
|
but there are still a few writes not yet do-able with MNC |
1749 |
|
(this is in progress) |
1750 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
1751 |
|
documentation will soon follow |
1752 |
|
- numerous small formatting cleanups for ProTeX |
1753 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
1754 |
|
|
1755 |
|
checkpoint54e_post |
1756 |
|
o add two new packages |
1757 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
1758 |
|
stratification dependent mixing |
1759 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
1760 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
1761 |
|
course), however there is only one diffusivity that is used for both |
1762 |
|
temperature and salinity (and passive tracers)ç |
1763 |
|
o add offline package |
1764 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
1765 |
|
provided by Stephanie Dutkiewicz |
1766 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
1767 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
1768 |
|
|
1769 |
|
checkpoint54d_post |
1770 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
1771 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
1772 |
|
leading to additional shift by 5 days each year of integration |
1773 |
|
(i.e. leading to considerable offset over the years) |
1774 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
1775 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
1776 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
1777 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
1778 |
|
(external loading & cpl import/export stay in forward_step.F) |
1779 |
|
o update coupling interface to work with new staggerTimeStep |
1780 |
|
o change MDSIO ptracers_pickup. |
1781 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
1782 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
1783 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
1784 |
|
|
1785 |
|
checkpoint54c_post |
1786 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
1787 |
|
this affects (truncation error) output.txt of test-exp: |
1788 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
1789 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
1790 |
|
o change Qnet to always be the net heat flux, (+upward). |
1791 |
|
affects (truncation error) output of natl_box exp.: updated |
1792 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
1793 |
|
o start to test mnc routinely in exp0 |
1794 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
1795 |
|
|
1796 |
|
checkpoint54b_post |
1797 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
1798 |
|
impressive on Altix and Opteron systems) |
1799 |
|
o diagnostics can now write NetCDF files through the mnc package |
1800 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
1801 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
1802 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
1803 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
1804 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
1805 |
|
|
1806 |
|
checkpoint54a_post |
1807 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
1808 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
1809 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
1810 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
1811 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
1812 |
|
checkpoint54a_pre |
1813 |
|
|
1814 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
1815 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
1816 |
|
|
1817 |
|
checkpoint54 |
1818 |
|
checkpoint53g_post |
1819 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
1820 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
1821 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
1822 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
1823 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
1824 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
1825 |
|
o restore adjointability |
1826 |
|
|
1827 |
|
checkpoint53f_post |
1828 |
|
o modifications that affect AIM experiment results (update output.txt): |
1829 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
1830 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
1831 |
|
o AIM pkg: |
1832 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
1833 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
1834 |
|
|
1835 |
|
checkpoint53e_post |
1836 |
|
o merged cylindrical coord configuration |
1837 |
|
o added rotating_tank experiment |
1838 |
|
checkpoint53e_pre |
1839 |
|
|
1840 |
|
checkpoint53d_post |
1841 |
|
o faulks upgraded: re-generate output.txt that have changed: |
1842 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
1843 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
1844 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
1845 |
|
o added Sadourny discretization of Coriolis |
1846 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
1847 |
|
- re-enabled use of omega3 (useAbsVorticity) |
1848 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
1849 |
|
vector-invariant equations |
1850 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
1851 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
1852 |
|
hopefully without new bugs |
1853 |
|
- still to do: biharmonic friction for non-hydrostatic w |
1854 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
1855 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
1856 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
1857 |
|
of mom_common/ |
1858 |
|
- simple re-arrangement of instructions within computing loop |
1859 |
|
checkpoint53d_pre |
1860 |
|
|
1861 |
|
checkpoint53c_post |
1862 |
|
o new version of coupler for AIM+thSIce and Ocean models |
1863 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
1864 |
|
- land: change Evaporation of snow |
1865 |
|
- aim with thSIce: fix bug in snow-precip. |
1866 |
|
o changes to calc_gw.F |
1867 |
|
- bug fix for w^2 term near the bottom boundary |
1868 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
1869 |
|
partial/looped cells |
1870 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
1871 |
|
and plume on slope), change the lateral boundary condition from half slip |
1872 |
|
to the value of no_slip_sides |
1873 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
1874 |
|
o Adjoint of EBM package + verification |
1875 |
|
* TLM OK |
1876 |
|
* ADM not sufficient accuracy yet (needs further testing) |
1877 |
|
|
1878 |
|
checkpoint53b_post |
1879 |
|
o Commiting new energy balance model to repository |
1880 |
|
* package is pkg/ebm |
1881 |
|
* verif. is verification/global_ocean_ebm |
1882 |
|
* references are in ebm_driver.F |
1883 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
1884 |
|
C Global thermohaline circulation. Part I: |
1885 |
|
C Sensitivity to atmospheric moisture transport. |
1886 |
|
C J. Climate 12(1), 71-82 |
1887 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
1888 |
|
C Global thermohaline circulation. Part II: |
1889 |
|
C Sensitivity with interactive transport. |
1890 |
|
C J. Climate 12(1), 83-91 |
1891 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
1892 |
|
C Destabilization of the thermohaline circulation |
1893 |
|
C by atmospheric eddy transports. |
1894 |
|
C J. Climate 7(12), 1870-1882 |
1895 |
|
o Will need long integration testing. |
1896 |
|
checkpoint53b_pre |
1897 |
|
|
1898 |
|
o created pkg/mom_common in preparation for variable viscosity code |
1899 |
|
o renamed and split ini_mnc_io |
1900 |
|
o pkg/land: only liquid water can diffuse or run-off |
1901 |
|
o AIM using land: soil wetness availability account for snow |
1902 |
|
o added printMapIncludesZeros to EEPARMS namelist |
1903 |
|
|
1904 |
|
checkpoint53a_post |
1905 |
|
o restore TAMC compatiility for exf_constants.h |
1906 |
|
(no usage of _d in .h) |
1907 |
|
o Additional storing in KPP in an attempt to fix |
1908 |
|
TAMC problem with adjoint of KPP code. |
1909 |
|
(no success...) |
1910 |
|
Identical code works fine with TAF. |
1911 |
|
o Fixed verification/natl_box_adjoint experiments. |
1912 |
|
Initial conditions for Experiments 4 and 5 are now |
1913 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
1914 |
|
and hence gives results closer to that of Experiment 2. |
1915 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
1916 |
|
|
1917 |
|
checkpoint53 |
1918 |
|
o stable checkpoint with up to date adjoint |
1919 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
1920 |
|
this is a code problem or a problem with resetting code for g_ |
1921 |
|
variables that is being autogenerated wrong. |
1922 |
|
Otherwise: |
1923 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
1924 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
1925 |
|
are both still in chaos following their security messes. |
1926 |
|
|
1927 |
|
checkpoint52n_post |
1928 |
|
o various build (mostly genmake2) changes including: |
1929 |
|
- ability to build/run more easily within Cygwin and MacOS X |
1930 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
1931 |
|
o pkg/seaice modifications |
1932 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
1933 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
1934 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
1935 |
|
- changed proxy for geostrophic velocity and updated |
1936 |
|
verification/lab_sea/results/* accordingly |
1937 |
|
- removed ADI dynamic solver from pkg/seaice |
1938 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
1939 |
|
they caused a segmentation fault under certain circumstances |
1940 |
|
- removed unused field WATR |
1941 |
|
o bug fix in exf-package: |
1942 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
1943 |
|
now reflect that. |
1944 |
|
o small fixes in the cal-package: |
1945 |
|
- set reference date to first of January for the 'model'-calendar |
1946 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
1947 |
|
warning |
1948 |
|
o small modifications in exf-package to increase flexibility: |
1949 |
|
- change climtempfreeze from a constant to a runtime parameter that |
1950 |
|
is specified in data.exf_clim (default = -1.9) |
1951 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
1952 |
|
specified in data.exf |
1953 |
|
o fix in pkg/thsice: |
1954 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
1955 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
1956 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
1957 |
|
|
1958 |
|
checkpoint52m_post |
1959 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
1960 |
|
this does not change any of the results, because myIter=0 in swfrac always |
1961 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
1962 |
|
as a default |
1963 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
1964 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
1965 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
1966 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
1967 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
1968 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
1969 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
1970 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
1971 |
|
o monitor package can write to NetCDF files and/or STDOUT |
1972 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
1973 |
|
o doc/api_reference added |
1974 |
|
- a framework for building an API Reference Manual using all |
1975 |
|
the "protex" comments embedded in the code |
1976 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
1977 |
|
o MNC: |
1978 |
|
- make myThid the last argument for all subroutines |
1979 |
|
- new default for the grid files: NO halos |
1980 |
|
- add useMNC and other run-time flags |
1981 |
|
- separate per-file-group handling of the unlimited dimension |
1982 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
1983 |
|
and lookup tables set in initialize_fixed |
1984 |
|
- write all MNC output to a freshly-created directory |
1985 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
1986 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
1987 |
|
o Added functionality to grdchk: |
1988 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
1989 |
|
|
1990 |
|
checkpoint52l_post |
1991 |
|
o new land formulation: |
1992 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
1993 |
|
energy conservation. |
1994 |
|
b) account for water temperature and for latent heat of freezing |
1995 |
|
in all processes (rain, run-off, ground storage) |
1996 |
|
c) compute surface and ground temperature implicitly. |
1997 |
|
o aim_v23 modification for new land model: |
1998 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
1999 |
|
to allow implicit computation of land & sea-ice surface temp. |
2000 |
|
b) add snow precipitation. |
2001 |
|
checkpoint52l_pre |
2002 |
|
|
2003 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
2004 |
|
o fix bug in timeAve (u,vZetatave in common block) |
2005 |
|
o no restoring terms under ice for pkg/seaice |
2006 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
2007 |
|
o bug fix for pkg/seaice pickups |
2008 |
|
o change MNC call locations and add coordinate attributes |
2009 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
2010 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
2011 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
2012 |
|
o exf: Adding simple range check routine for exf fields after read |
2013 |
|
|
2014 |
|
checkpoint52k_post |
2015 |
|
o removed top-level directory "diags" |
2016 |
|
- we migrated these functions to pkg/timeave a long time ago |
2017 |
|
o fixed bug introduced in pkg/monitor |
2018 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
2019 |
|
averaged fields (I/O via cost_averages) |
2020 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
2021 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
2022 |
|
o added initial do_the_model_io to ecco |
2023 |
|
o set all ...Freq to zero after cost_final |
2024 |
|
taveFreq, dumpFreq, pChkptFreq |
2025 |
|
o MAIN and ECCO differentiability restored |
2026 |
|
|
2027 |
|
checkpoint52j_post |
2028 |
|
o fix nchklev in tamc.h for global_ocean... |
2029 |
|
o Bringing flow and store directives up-to-date |
2030 |
|
o Really weird thing! |
2031 |
|
call do_the_model_io from the_main_loop with parameters |
2032 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
2033 |
|
TAF places a faulty re-call of initialise_varia |
2034 |
|
after cost_final call which should not be there! |
2035 |
|
checkpoint52j_pre |
2036 |
|
|
2037 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
2038 |
|
error messages |
2039 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
2040 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
2041 |
|
debug output |
2042 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
2043 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
2044 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
2045 |
|
o update AIM Equatorial Channel exp: |
2046 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
2047 |
|
o globalFile now works with exch2 |
2048 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
2049 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
2050 |
|
o limit timeave output for hi-res integrations |
2051 |
|
|
2052 |
checkpoint52i_post |
checkpoint52i_post |
2053 |
o removed CPP_EEOPTIONS.h from verification/*/code |
o removed CPP_EEOPTIONS.h from verification/*/code |
2054 |
o updated the tiling for global_ocean_pressure |
o updated the tiling for global_ocean_pressure |