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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
6 |
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7 |
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o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
8 |
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on CS-grid: no longer loosing mass. |
9 |
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o exf & curvilinear-grid: no longer modify longitude xC & xG. |
10 |
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o pkg/ggl90: fix sloppy output and fix a bug |
11 |
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o pkg/seaice: added SEAICEuseEVPpickup parameter |
12 |
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- Set to false in order to start EVP solver with |
13 |
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non-EVP pickup files when using SEAICEuseEVP |
14 |
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- fix sign error in diffusion in seaice_calc_rhs |
15 |
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|
16 |
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checkpoint58h_post |
17 |
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* Modifications for bottom topography control |
18 |
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o replace hFacC by _hFacC at various places |
19 |
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o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
20 |
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o add non-self-adjoint cg2d_nsa |
21 |
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o update autodiff support routines |
22 |
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o re-initialise hfac after ctrl_depth_ini |
23 |
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o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
24 |
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* Adding verification for 5x5 box (4-layer) bottom topography control |
25 |
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|
26 |
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checkpoint58g_post |
27 |
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o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
28 |
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used for mean seasonal cycle, mean diurnal cycle); add an example |
29 |
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in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
30 |
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o pkg/ggl90: |
31 |
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- add parameter (minimum surface kinetic energy) |
32 |
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- fix bug (avoiding division by zero) |
33 |
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o couple pkg/thsice to pkg/seaice: |
34 |
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- modify advection in seaice to accomodate new scalar fields to be advected |
35 |
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- only muliDimAdection scheme work with seaice/thsice |
36 |
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- mapping of thsice-variables to seaice-variables, back and forth |
37 |
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- does not break the verification experiments, but does not give the |
38 |
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desired results either |
39 |
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o pkg/seaice |
40 |
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- make (default) second order advection a bit less confusing? |
41 |
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|
42 |
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checkpoint58f_post |
43 |
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o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
44 |
|
to pkg/seaice): |
45 |
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- new routines thsice_map_exf and thsice_get_exf provide the interface |
46 |
|
- add an additional formal parameter to thsice_solve4temp |
47 |
|
o pkg/exf: |
48 |
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- add new fields wspeed, snowprecip (to be able to couple to thsice) |
49 |
|
- correct Stefan-Boltzmann constant |
50 |
|
- new parameter for longwave surface emittance |
51 |
|
- separate some stuff from exf_bulkformulae into new routines |
52 |
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exf_radiation, exf_wind |
53 |
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- add new parameters and constants: longwave emissivity for ocean, ice |
54 |
|
and snow, evaporation parameters over ice |
55 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
56 |
|
either wind from stress or stress from wind |
57 |
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o pkg/thSIce: |
58 |
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- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
59 |
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- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
60 |
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and THSICE_CALC_THICKN |
61 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
62 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
63 |
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to make debugging easier. |
64 |
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- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
65 |
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o pkg/bulk_force: |
66 |
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- clean-up comments and parameters ; |
67 |
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- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
68 |
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o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
69 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
70 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
71 |
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testreport accordingly |
72 |
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|
73 |
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checkpoint58e_post |
74 |
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o SEAICE_CGRID adjoint done |
75 |
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o R_STAR adjoint implemented. |
76 |
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* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
77 |
|
* need to sort out init. of h0facc, etc. |
78 |
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o Make pkg/profile fully independent of ecco,cost, etc. stuff |
79 |
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to be able to use it in pure forward. |
80 |
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|
81 |
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checkpoint58d_post |
82 |
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o upgrade simple test-experiment to tutorial example: |
83 |
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step.1: duplicate the experiment and (step.2) will remove the old copy. |
84 |
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tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
85 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
86 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
87 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
88 |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
89 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
90 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
91 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
92 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
93 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
94 |
|
o correct a sign problem in cost_scat.F |
95 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
96 |
|
with larger stencil |
97 |
|
o thsice adjoint: start |
98 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
99 |
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completeness |
100 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
101 |
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and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
102 |
|
o ptracers adjoint: |
103 |
|
* avoid extensive recomputatations |
104 |
|
* fix missing re-init. of gptr (missed by TAF) |
105 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
106 |
|
me to turn off the excessive output to STDOUT that this package produces |
107 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
108 |
|
and add those terms in Vector-Invariant formulation. |
109 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
110 |
|
if the control period (xx_hfluxperiod etc) is 0 |
111 |
|
o in profiles pkg, clean routines and fix details |
112 |
|
o in ecco pkg, reading ssh data: |
113 |
|
fix problem in case the model does not start at iter0=0 |
114 |
|
o fix mnc-pickup/restart for ptracers |
115 |
|
o new package prifiles: |
116 |
|
code to compute profile-based cost by Gael Forget |
117 |
|
(modifs in ecco, ctrl, autodiff) |
118 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
119 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
120 |
|
|
121 |
|
checkpoint58c_post |
122 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
123 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
124 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
125 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
126 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
127 |
|
with SEAICE_CGRID defined. |
128 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
129 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
130 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
131 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
132 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
133 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
134 |
|
o fix bug in quasihydrostatic S/R ; |
135 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
136 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
137 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
138 |
|
o add on/off flag useOffLine for package OFFLINE |
139 |
|
o seaice: |
140 |
|
- modify advection so that it works also on the C-grid |
141 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
142 |
|
problem in multi-tile runs with C-grid |
143 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
144 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
145 |
|
C-grid solver |
146 |
|
- added a few comments to seaice_diffusion.F |
147 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
148 |
|
are now exclusive) |
149 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
150 |
|
required re-ordering the code a little: |
151 |
|
+ make DAIRN global variable (defined in SEAICE) |
152 |
|
+ move computation of the viscosities eta and zeta into a new separate |
153 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
154 |
|
|
155 |
|
checkpoint58b_post |
156 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
157 |
|
update output.txt of exp. aim.5l_cs.thSI |
158 |
|
o various mnc cleanups and improvements: |
159 |
|
+ shrink lookup tables by factor of ~4 |
160 |
|
+ better error reporting when running out of lookup space |
161 |
|
+ able to handle longer path/file names (up to 500 chars) |
162 |
|
o adjoint: |
163 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
164 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
165 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
166 |
|
(allow to differentiate between forcing components using new integer flags: |
167 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
168 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
169 |
|
o ecco |
170 |
|
- enable trend removal from SSH anomaly obs. |
171 |
|
o adjoint |
172 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
173 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
174 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
175 |
|
(NLFS seems broken sometimes after I checked it in) |
176 |
|
o seaice: |
177 |
|
- add c-grid version of the dynamic solver: |
178 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
179 |
|
and ostres |
180 |
|
+ put a few fields that were local to dynsolver into global common |
181 |
|
blocks, so that I can move the computation of stresses etc into |
182 |
|
seaice_lsr (saves coding but may break the adjoint). |
183 |
|
- replace more hardwired parameters by runtime parameters |
184 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
185 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
186 |
|
if this works properly), eventually this should replace the clipping |
187 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
188 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
189 |
|
include it only where its needed |
190 |
|
o move balancing of fluxes before the call of external_forcing_surf |
191 |
|
o seaice: |
192 |
|
- correct units of turning angles (now they are really in degrees) |
193 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
194 |
|
- initialize GWATX/Y in seaice_init |
195 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
196 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
197 |
|
o seaice: add runtime flags for turning angles (default to zero) |
198 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
199 |
|
and trend from exf forcing and ctrl control adjustments |
200 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
201 |
|
(since checkpoint57x_post) |
202 |
|
o change the default rotation period to 86164.s = the Earth rotation |
203 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
204 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
205 |
|
o seaice advection: add code for choosing between the default (2nd order |
206 |
|
central differences) and multiDim advection schemes provided by |
207 |
|
pkg/generic_advdiff |
208 |
|
o seaice: |
209 |
|
- removed all references to SEAICE_GRID.h fields from |
210 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
211 |
|
(cubed-sphere configuration will change a little) |
212 |
|
- grid computations in seaice_init are obsolete now. |
213 |
|
- cleaned up code a little so that is easier to read (hopefully). |
214 |
|
- added new (better?) discretizations of default advection and diffusion |
215 |
|
(turn on with SEAICEuseFluxForm) |
216 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
217 |
|
|
218 |
|
checkpoint58a_post |
219 |
|
o seaice: |
220 |
|
- bug fix in advect.F |
221 |
|
o shelfice: |
222 |
|
- separate shelfice load anomaly from pload (breaks with time |
223 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
224 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
225 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
226 |
|
done offline. A good approximation of the pressure load anomaly is |
227 |
|
necessary to avoid large initial adjustment processes underneath |
228 |
|
deep-reaching shelfice. |
229 |
|
- small fix in ISOMIP shelfice_thermodynamics |
230 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
231 |
|
now the default |
232 |
|
- give a few constants more intuitive names |
233 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
234 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
235 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
236 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
237 |
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STDOUT. |
238 |
|
o fix bug (typo) in obcs_apply_eta.F |
239 |
|
o add a new package shelfice which enables us to model the circulation |
240 |
|
underneath shelf-ice with draughts of hundreds of meters. |
241 |
|
- works |
242 |
|
- to do: + include improved thermodynamics |
243 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
244 |
|
instead of new field kTopC |
245 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
246 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
247 |
|
and ini_mask_etc.F? |
248 |
|
+ adjust vertical mixing schemes? |
249 |
|
o seaice pkg: |
250 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
251 |
|
freezing point of sea water at the surface |
252 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
253 |
|
meridional stresses are now different (and hopefully correct) |
254 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
255 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
256 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
257 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
258 |
|
diagnostics ; define regions by reading a region-mask from a file |
259 |
|
(might add other options later) |
260 |
|
o pkg/bulk_force: |
261 |
|
- add option and parameters to use AIM surface-flux formulae. |
262 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
263 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
264 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
265 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
266 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
267 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
268 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
269 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
270 |
|
|
271 |
|
checkpoint58 |
272 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
273 |
|
tools can be compiled (as determined by genmake2) will turn on the |
274 |
|
embed_files package which then embeds the entire MITgcm source code |
275 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
276 |
|
- requested by CNH but off by default |
277 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
278 |
|
- only writes the output when useEMBEDSRC in eedata is true |
279 |
|
o clean up 3-dim. relaxation codes: |
280 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
281 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
282 |
|
* Thanks to Tom Haine for testing! |
283 |
|
|
284 |
|
checkpoint57z_post |
285 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
286 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
287 |
|
o fix the pickup behavior for obcs in combination with ptracers |
288 |
|
o fix a bug in ptracers_external_fields_load |
289 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
290 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
291 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
292 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
293 |
|
and update lab_sea output.txt file. |
294 |
|
o completing 3-dim. relaxation code: additional term |
295 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
296 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
297 |
|
* At compile time, in "EXF_OPTIONS.h" set |
298 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
299 |
|
#define ALLOW_CLIMSALT_RELAXATION |
300 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
301 |
|
tauThetaClimRelax3Dim = 15552000.0, |
302 |
|
tauSaltClimRelax3Dim = 15552000.0, |
303 |
|
* 3 cases: |
304 |
|
1) Use a constant-in-time 3-dim. field |
305 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
306 |
|
3) Real-time relax. to time-evolving prescribed field |
307 |
|
o Adding Laplacian-type smoothness constraint on |
308 |
|
initial and boundary (forcing) controls (ic, bc) |
309 |
|
* enable at compile-time via |
310 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
311 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
312 |
|
* Absolute scale somewhat unclear so far |
313 |
|
* no area weighting was included since no other cost term does so far |
314 |
|
|
315 |
|
checkpoint57y_post |
316 |
|
First step for a NLFS adjoint |
317 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
318 |
|
o new init. routines for calc_r_star, calc_surf_dr |
319 |
|
o still need to deal with ini_masks_etc |
320 |
|
o testreport seemed happy |
321 |
|
checkpoint57y_pre |
322 |
|
|
323 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
324 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
325 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
326 |
|
o cfc fixes for final year of integration |
327 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
328 |
|
be in GCHEM_OPTIONS). |
329 |
|
|
330 |
|
checkpoint57x_post |
331 |
|
o fix testreport Pb in multiple test experiment. |
332 |
|
o cleanup our namelist syntax in verification: |
333 |
|
- make it more F95 standards compliant (some work still needed) |
334 |
|
- allows the vast majority of our tests to work with gfortran |
335 |
|
o Non-Hydrostatic: |
336 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
337 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
338 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
339 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
340 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
341 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
342 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
343 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
344 |
|
o remove some unused variables (reduces number of compiler warnings) |
345 |
|
o adjoint |
346 |
|
* Disable useVariableViscosity for adjoint for time being |
347 |
|
(there are a number of extensive recomputations) |
348 |
|
* Initialize certain variables needed for adjoint |
349 |
|
|
350 |
|
checkpoint57w_post |
351 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
352 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
353 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
354 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
355 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
356 |
|
o tracer advection scheme: |
357 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
358 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
359 |
|
was not very convenient). |
360 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
361 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
362 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
363 |
|
and sRef for convenience, handy, when you want to initialize |
364 |
|
ptracers in a large domain with a constant non-zero value. Also, |
365 |
|
untangle ptracers_init.F a little. |
366 |
|
|
367 |
|
checkpoint57v_post |
368 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
369 |
|
o remove all the files from the cfc_offline test since they are now |
370 |
|
incorporated into tutorial_cfc_offline which has been producing |
371 |
|
identical results for a few days of testing |
372 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
373 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
374 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
375 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
376 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
377 |
|
o vorticity & strain are now computed without masking, to account for |
378 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
379 |
|
anyway later on, before computing advection/coriolis terms. |
380 |
|
o modify exp4 to test new obcs support for reading from external files |
381 |
|
and for passive tracers |
382 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
383 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
384 |
|
file). |
385 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
386 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
387 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
388 |
|
to be proportional to enstrophy dissipation length. Thus, |
389 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
390 |
|
This is now consistent with Smagorinsky and with the manual. |
391 |
|
|
392 |
|
checkpoint57u_post |
393 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
394 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
395 |
|
OB-values from file; this is not different from the way theta and salinity |
396 |
|
are treated |
397 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
398 |
|
will stop if you use pTracers and Orlanski at the same time. |
399 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
400 |
|
boundary values are overwritten with values from files for which there |
401 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
402 |
|
it possible to use different OBs at different ends of the domain (as |
403 |
|
with EXF) |
404 |
|
o reduce number of exch calls in shap_filt (s2). |
405 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
406 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
407 |
|
|
408 |
|
checkpoint57t_post |
409 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
410 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
411 |
|
same truncation, independent of the face number: affects affects several |
412 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
413 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
414 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
415 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
416 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
417 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
418 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
419 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
420 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
421 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
422 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
423 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
424 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
425 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
426 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
427 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
428 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
429 |
|
Many new viscosity diagnostics available. |
430 |
|
|
431 |
|
checkpoint57s_post |
432 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
433 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
434 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
435 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
436 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
437 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
438 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
439 |
|
ViscAhStrain and viscAhTension are now retired. |
440 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
441 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
442 |
|
that it finds in the *current* directory when searching for files. |
443 |
|
Soft-links found in any other source directories will still work as |
444 |
|
they did before. |
445 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
446 |
|
a C routine to unlimit the stack size |
447 |
|
o mnc-ify pkg/aim snapshot vars |
448 |
|
o mnc-ify pkg/land as requested by Daniel |
449 |
|
o various changes to mnc including: |
450 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
451 |
|
- output can now be grouped so that all files within a group |
452 |
|
change the ITER portion of their names in lock-step together |
453 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
454 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
455 |
|
- writing works for all verification test cases w/ g77 on Linux |
456 |
|
|
457 |
|
checkpoint57r_post |
458 |
|
o make MNC variable initialization happen earlier |
459 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
460 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
461 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
462 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
463 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
464 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
465 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
466 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
467 |
|
o add time-dependent SST, SSS control |
468 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
469 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
470 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
471 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
472 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
473 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
474 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
475 |
|
(see README file) |
476 |
|
|
477 |
|
checkpoint57q_post |
478 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
479 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
480 |
|
- bug was reported by Jean-Michel and Ian Fenty |
481 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
482 |
|
update exp. cpl_aim+ocn output. |
483 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
484 |
|
Needed for high-res. runs with large global files |
485 |
|
to be able to limit tapelev size |
486 |
|
o Changed some tests for adjoint: |
487 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
488 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
489 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
490 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
491 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
492 |
|
* converts, compiles and runs successfully; |
493 |
|
|
494 |
|
checkpoint57p_post |
495 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
496 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
497 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
498 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
499 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
500 |
|
(was already the case for dissipation with mom_vecinv, |
501 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
502 |
|
This will allow to put dissipation out-off the AB time-stepping. |
503 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
504 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
505 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
506 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
507 |
|
|
508 |
|
checkpoint57o_post |
509 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
510 |
|
(2) its ready to be documented during the 20050801 DocFest |
511 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
512 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
513 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
514 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
515 |
|
(worth another tag) |
516 |
|
|
517 |
|
checkpoint57n_post |
518 |
|
o adding precip control xx_precip 32 |
519 |
|
o adding swflux control xx_swflux 33 |
520 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
521 |
|
o Implementing partitioning in time-mean and variable adjustment |
522 |
|
for atmos. state. |
523 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
524 |
|
o in natl_box_adjoint: |
525 |
|
* updated exp 1 to 10 |
526 |
|
(but does not have time-mean vs. variable split results yet) |
527 |
|
o updated global1x1/*_seaice_adj/ |
528 |
|
to incorporate latest changes |
529 |
|
o enable useSingleCpuIO for mdsio vector routines |
530 |
|
(applies in particular to tapelev I/O) |
531 |
|
o removed inefficient K-loop in all active_file*control*.F |
532 |
|
|
533 |
|
checkpoint57m_post |
534 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
535 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
536 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
537 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
538 |
|
|
539 |
|
checkpoint57l_post |
540 |
|
tag before updating tutorials (pre-release-2) |
541 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
542 |
|
for output and interpolation of input fields onto model grid) |
543 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
544 |
|
Affects results of exp. rotating_tank ; update output.txt. |
545 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
546 |
|
and taking the square quantity and/or using a fraction-weight field. |
547 |
|
o fix aim_diagnostics_init.F mate numbers. |
548 |
|
o add mnc output capability to diagnostics/diagstat and update |
549 |
|
our cvsignore files for the ACSII output generated |
550 |
|
|
551 |
|
checkpoint57k_post |
552 |
|
o lab_sea now uses diagnostics package and provides a suite of |
553 |
|
new EXF diagnostics output. |
554 |
|
|
555 |
|
checkpoint57j_post |
556 |
|
o exf |
557 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
558 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
559 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
560 |
|
* extended diagnostics output |
561 |
|
- now includes all EXF variables |
562 |
|
- hs, hl moved to common block |
563 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
564 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
565 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
566 |
|
* updated verif. lab_sea, global_with_exf |
567 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
568 |
|
to ensure that diagnostics sees a true EXFqnet |
569 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
570 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
571 |
|
several times with different frequencies. |
572 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
573 |
|
- the monitor--MNC output needs work |
574 |
|
- many attributes need to be added (most are currently blank) |
575 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
576 |
|
- many attributes need to be added (most are currently blank) |
577 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
578 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
579 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
580 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
581 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
582 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
583 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
584 |
|
|
585 |
|
checkpoint57i_post |
586 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
587 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
588 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
589 |
|
add 1rst Order upwind vertical Shear. |
590 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
591 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
592 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
593 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
594 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
595 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
596 |
|
some "_d 0", etc. no effect. |
597 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
598 |
|
separate 'iter' variable for iteration count |
599 |
|
o pkg/diagnostics: |
600 |
|
add new capability: output of Global/Regional & per-level statistics ; |
601 |
|
tested against monitor output (including land & thSIce) on various exp. |
602 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
603 |
|
|
604 |
|
checkpoint57h_done |
605 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
606 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
607 |
|
|
608 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
609 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
610 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
611 |
|
and rename it: DIFFERENT_MULTIPLE |
612 |
|
|
613 |
|
checkpoint57h_post |
614 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
615 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
616 |
|
of Nb of iterations). This requires to change data.diagnostics. |
617 |
|
checkpoint57h_pre |
618 |
|
|
619 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
620 |
|
and mnc_outdir_num are false |
621 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
622 |
|
per-file basis, the file precision [default behavior is unchanged] |
623 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
624 |
|
depth based on a temperature/density criterion |
625 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
626 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
627 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
628 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
629 |
|
not mnc -- this mistake was found by JMC and is now corrected |
630 |
|
|
631 |
|
checkpoint57g_post |
632 |
|
o add Adams-Bashforth 3rd Order time stepping: |
633 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
634 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
635 |
|
checkpoint57g_pre |
636 |
|
|
637 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
638 |
|
(default remains spatially uniform constant based on tau) |
639 |
|
o added new control variables |
640 |
|
* init. uVel, vVel, etanN |
641 |
|
* lambda[Theta,Salt]ClimRelax |
642 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
643 |
|
(suggested by G. Forget) |
644 |
|
|
645 |
|
checkpoint57f_post |
646 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
647 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
648 |
|
account for baseTime shift |
649 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
650 |
|
checkpoint57f_pre |
651 |
|
|
652 |
|
o mnc-ifying the seaice package |
653 |
|
o introduced an alternative length scale calculation for use in the limiting |
654 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
655 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
656 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
657 |
|
as well as grad(vort3). Made it compatible with both approximate form |
658 |
|
for the cubed sphere and full form of these gradients. Added flag |
659 |
|
useFullLeith to select between approximate and full form. |
660 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
661 |
|
update output.txt of exp. fizhi-gridalt-hs |
662 |
|
o change port_rand funtion to allow to set the seed. |
663 |
|
o fix obscure MNC bug involving conversion between reals and integers |
664 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
665 |
|
new version is now more standards-compliant |
666 |
|
o adjoint-related modifications |
667 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
668 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
669 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
670 |
|
|
671 |
|
checkpoint57e_post |
672 |
|
o Adding eddy stress controls a la Ferreira et al. |
673 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
674 |
|
|
675 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
676 |
|
update output.txt of exp. fizhi-gridalt-hs |
677 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
678 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
679 |
|
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
680 |
|
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
681 |
|
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
682 |
|
months and years. Requires pkg/cal. |
683 |
|
o diagnostics: add pickup functionality |
684 |
|
- off by default for backwards compatibility |
685 |
|
- current version only uses MDSIO -- MNC will be added |
686 |
|
o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
687 |
|
o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
688 |
|
|
689 |
|
checkpoint57d_post |
690 |
|
o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
691 |
|
o modify verification/ideal_2D_oce so that it tests the creation of mnc |
692 |
|
output from the diagnostics package |
693 |
|
o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
694 |
|
o make genmake2 more portable by using ".$FS" instead of ".f" for more |
695 |
|
of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
696 |
|
o add coordinate variables to the MNC output from the diagnostics package |
697 |
|
o change MNC-flags default value: true when useMNC=TRUE |
698 |
|
o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
699 |
|
the ability (off by default) to read the grid information using MNC |
700 |
|
o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
701 |
|
o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
702 |
|
o do snap-shot diagnostics at the middle of the time-interval (instead of |
703 |
|
at the end). |
704 |
|
o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
705 |
|
new test for AIM with thSIce + slab-ocean |
706 |
|
o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
707 |
|
o move state variable diagnostics to the beginning of the time step ; |
708 |
|
(note: still needs some work specially for snap-shot diagnostics) |
709 |
|
duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
710 |
|
|
711 |
|
checkpoint57c_post |
712 |
|
o Change testing option (-ieee) to get closer agreement between g77 & ifort |
713 |
|
o generate new output.txt files on faulks with g77 & the new -ieee option |
714 |
|
checkpoint57c_pre |
715 |
|
|
716 |
|
o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
717 |
|
update output.txt of exp. global_ocean.90x40x15 |
718 |
|
o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
719 |
|
results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
720 |
|
o add saltFlux(+File) forcing capability with periodicExternalForcing |
721 |
|
o allow to use pkg diagnostics for GM-Redi & ThSIce output |
722 |
|
o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
723 |
|
o improvements for the MNC output from DIAGNOSTICS: |
724 |
|
- correct handling of the unlimitied dimension |
725 |
|
- all dims now have associated coordinate variables |
726 |
|
- variables located at U, V, and Corner ("Z") points are now written |
727 |
|
with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
728 |
|
*all* data points are output |
729 |
|
o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
730 |
|
o added pkg/seaice/seaice_monitor.F |
731 |
|
o mdsio_readfield.F can now read files visible only to master MPI process. |
732 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
733 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
734 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
735 |
|
spurious negative numbers for precipitation and humidity. Will cause |
736 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
737 |
|
o pkg/ctrl/ |
738 |
|
* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
739 |
|
May be enabled via doPackDiag |
740 |
|
* introduce z-scaling of |
741 |
|
+ gradient (doZscalePack) and |
742 |
|
+ control (doZscaleUnpack) |
743 |
|
o pkg/mdsio/ |
744 |
|
* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
745 |
|
* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
746 |
|
|
747 |
|
checkpoint57b_post |
748 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
749 |
|
o fix MNC coordinate variables so that they now contain per-face index |
750 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
751 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
752 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
753 |
|
o Implement instantaneous output within pkg diagnostics: |
754 |
|
setting a negative frequency in data.diagnostics produces |
755 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
756 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
757 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
758 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
759 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
760 |
|
becomes the coordinate variable for the 'T' dimension |
761 |
|
o add CF-style coordinate variables to MNC |
762 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
763 |
|
missing along the T axis but otherwise it works! |
764 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
765 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
766 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
767 |
|
this is based directly on what the model compute, so that the content of |
768 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
769 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
770 |
|
o clean up build options files for SunOS, in particular |
771 |
|
- remove -traditional from xmakedepend |
772 |
|
- change -xarch=v9 to -xarch=native for f77 |
773 |
|
- restore use of make (not gmake) |
774 |
|
- add CC=gcc if using g77 |
775 |
|
o changes per discussion of AM, JMC, & EH3 today: |
776 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
777 |
|
creating proper CF-style coordinate variables and in recognition |
778 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
779 |
|
the grid files into any of the other NetCDF files |
780 |
|
- *always* output grid variables with MDSIO (this will eventually be |
781 |
|
changed) |
782 |
|
- output MNC grid file if useMNC is true |
783 |
|
o every instance of _END_MASTER() has been found and replaced with |
784 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
785 |
|
preprocessors |
786 |
|
o re-arrange diagnostics pkg initialisation: |
787 |
|
- allow each package to extend the available diagnostics list |
788 |
|
- add some checking and fix small problems (multi-threaded, ...) |
789 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
790 |
|
look through the short list of active diag. (instead of the long list) |
791 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
792 |
|
|
793 |
|
checkpoint57a_post |
794 |
|
o this set of changes restores TAMC compatibility |
795 |
|
tested for global_ocean.90x40x15 adjoint on trough |
796 |
|
(what a pain) |
797 |
|
|
798 |
|
checkpoint57a_pre |
799 |
|
o some modifs in tools/build_options for sunos |
800 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
801 |
|
|
802 |
|
checkpoint57 |
803 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
804 |
|
- new parameter viscA4W (defaults to viscA4) |
805 |
|
- affects only non-hydrostatic code |
806 |
|
- to be done: no-slip lateral boundary conditions |
807 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
808 |
|
o implement Implicit Vertical advection for pTracers |
809 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
810 |
|
(implemented also for implicit vertical diffusion & advection) |
811 |
|
o OBCS: extend application of tracer open boundary conditions |
812 |
|
to a strip beyond the boundary of width Olx/Oly |
813 |
|
o add call monitor to TAF set of required calls (flow directives) |
814 |
|
and include in natl_box_adjoint |
815 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
816 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
817 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
818 |
|
(theta2, salt2 in ecco_cost_weights) |
819 |
|
|
820 |
|
checkpoint56c_post |
821 |
|
o OBCS as control variables |
822 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
823 |
|
- remove balance of obcs controls from default |
824 |
|
- fix index bug nobcs in ctrl_init |
825 |
|
- fix dummy fields filen in ctrl_pack |
826 |
|
- add dummy weights for obcs |
827 |
|
o lsopt: comment out fort.94 output |
828 |
|
o optim: |
829 |
|
- remove unnecessary header files |
830 |
|
- adjusted namelists |
831 |
|
- add xerbla.F to Makefile |
832 |
|
o exf: |
833 |
|
- multiple modifications of exf_check_range |
834 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
835 |
|
o mdsio: |
836 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
837 |
|
|
838 |
|
checkpoint56b_post |
839 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
840 |
|
is called from DO_THE_MODEL_IO |
841 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
842 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
843 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
844 |
|
o add another verification experiment that tests both the cfc-pkg and |
845 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
846 |
|
reactive tendencies treated inline with regular timestepping |
847 |
|
o testreport previously did a lousy job of comparing small numbers, so |
848 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
849 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
850 |
|
testreport. |
851 |
|
o ptracers_monitor: bug fix for MPI |
852 |
|
|
853 |
|
checkpoint56a_post |
854 |
|
o GCHEM: finish reorganizating the package |
855 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
856 |
|
(introduces another 3D-array for each passive tracer, but only if |
857 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
858 |
|
gchemTendency is not needed because the timestep is done separately) |
859 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
860 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
861 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
862 |
|
so clear to me how that should be done in a general way. |
863 |
|
o CFC: improve formatting of output in CFC_ATMOS |
864 |
|
o PTRACERS: |
865 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
866 |
|
that ALL experiments with ptracers enable can be checked. This makes |
867 |
|
GCHEM_MONITOR obsolete. |
868 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
869 |
|
monitorFreq |
870 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
871 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
872 |
|
o exf_check_range: |
873 |
|
* default changed to .TRUE. |
874 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
875 |
|
* STOP in exf_check_range if 'out of range' |
876 |
|
* range chosen generous to allow for potential extema |
877 |
|
TBD: a version with stricter range |
878 |
|
permitted range would be runtime parameters |
879 |
|
o GMredi: |
880 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
881 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
882 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
883 |
|
o GCHEM: |
884 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
885 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
886 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
887 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
888 |
|
this flag is now only visible within GCHEM-pkg routines. |
889 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
890 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
891 |
|
this, the tracer ID iTracer had to be included into the parameter list |
892 |
|
of ptracers_forcing |
893 |
|
- set up forward_step to call gchem_forcing, that will replace |
894 |
|
gchem_forcing_int in ptracers_forcing |
895 |
|
- cleaning up |
896 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
897 |
|
|
898 |
|
checkpoint56 |
899 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
900 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
901 |
|
o ECCO-GODAE |
902 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
903 |
|
* fully merged and updated from SIO code |
904 |
|
windstress sign change affects |
905 |
|
- exf_inscal_[u/v]stress |
906 |
|
- sign of xx_tau[u/v] adjustments |
907 |
|
- signs in cost_scat |
908 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
909 |
|
* natl_box_adjoint updated and compressed |
910 |
|
* 2-level checkpoint switch added |
911 |
|
(tested in EXP. 1 of natl_box_adjoint) |
912 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
913 |
|
o SVD |
914 |
|
* first complete, non-hacked version for SVD calculations |
915 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
916 |
|
performed via direct access files admtlm_vector.it???? |
917 |
|
(via ctrl_[un]pack) |
918 |
|
* optimcycle is used for ARPACK iteration counter |
919 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
920 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
921 |
|
and add linear transforms where necessary |
922 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
923 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
924 |
|
o mdsio: filename info to both stderr, stdout |
925 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
926 |
|
from sign change |
927 |
|
|
928 |
|
checkpoint55j_post |
929 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
930 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
931 |
|
o add consistent build directories and .cvsignore files to verification |
932 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
933 |
|
o make all subroutines 30 or less characters in length for certain older |
934 |
|
compilers to work (a thorough search only turns up two routines in |
935 |
|
pkg/ptracers) |
936 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
937 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
938 |
|
|
939 |
|
checkpoint55i_post |
940 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
941 |
|
3.D if implicit) ; each ptracer uses its own background value. |
942 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
943 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
944 |
|
ITRDA and other clusters without the mpirun "-wd" option |
945 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
946 |
|
configuration |
947 |
|
o give MNC the ability to create additional files rather than |
948 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
949 |
|
- the default is just less than 2GB which is a practical limit |
950 |
|
on many systems |
951 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
952 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
953 |
|
|
954 |
|
checkpoint55h_post |
955 |
|
o add verification test "vermix" |
956 |
|
o remove all the *_ioinc flags and replace with the single global |
957 |
|
outputTypesInclusive flag |
958 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
959 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
960 |
|
o useMNC moved from data.mnc to data.pkg |
961 |
|
|
962 |
|
checkpoint55g_post |
963 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
964 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
965 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
966 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
967 |
|
Works well for global_ocean.90x40x15, |
968 |
|
but recomp. issue remains for carbon |
969 |
|
o Updating adjoint output for natl_box_adjoint after |
970 |
|
pkg/ecco has been modified (see taga c55d_post) |
971 |
|
|
972 |
|
checkpoint55f_post |
973 |
|
o rename to timeave_init_fixed |
974 |
|
|
975 |
|
checkpoint55e_post |
976 |
|
o some delicate re-shuffle of store directives to avoid one |
977 |
|
extra call of do_oceanic_physics |
978 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
979 |
|
checkpoint_lev1_directives.h |
980 |
|
o NB: this may break global_ocean adjoint temporarily, |
981 |
|
but it is clear how to fix it. Will do later, need this now. |
982 |
|
|
983 |
|
checkpoint55d_post |
984 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
985 |
|
o ecco_cost_weights is modified to 1x1 runs |
986 |
|
o modifs to allow observations to be read in as |
987 |
|
single file or yearly files |
988 |
|
o enable to read exf forcing fields as either |
989 |
|
single file or yearly files (flag useExfYearlyFields) |
990 |
|
checkpoint55d_pre |
991 |
|
|
992 |
|
o switch between 2-level and 3-level checkpointing |
993 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
994 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
995 |
|
with the correct (that is, the complete multi-dimensional) set of |
996 |
|
array indicies |
997 |
|
- used in mom_vecinv() to write the diagFreq output |
998 |
|
- tested (demonstrated) in verification/aim.5l_cs |
999 |
|
o further mnc-ification |
1000 |
|
- add verification/lab_sea to the list with mnc setups |
1001 |
|
- fix undefined mnc v-names in cd_code |
1002 |
|
- add kpp to mnc output (both snapshot and timeave) |
1003 |
|
o non-hydrostatic code |
1004 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
1005 |
|
in calc_gw.F |
1006 |
|
- defaults to viscAh |
1007 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
1008 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
1009 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
1010 |
|
o pkg/cost |
1011 |
|
extend simple cost functions to treat time mean quantities |
1012 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
1013 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
1014 |
|
be 2 times larger than the minimum size the advection scheme requires. |
1015 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
1016 |
|
o GGL90 (Gaspar's TKE mixed layer) |
1017 |
|
- add horizontal diffusion of TKE, requires exchanges in |
1018 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
1019 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
1020 |
|
mixing coefficients are computed from a horizontal average of TKE of |
1021 |
|
6 points or so. I think that diffusion has a little more physical |
1022 |
|
justification. |
1023 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
1024 |
|
was in vain) |
1025 |
|
- mask tke-variable in ggl90_init |
1026 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
1027 |
|
o fix biharmonic diffusion on CS-grid. |
1028 |
|
o more obcs stuff |
1029 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
1030 |
|
for reading boundary values. This routine is called from |
1031 |
|
obcs_prescribe_read |
1032 |
|
- updated obcs_check |
1033 |
|
- changed sponge layer relaxation parameter units for days to seconds |
1034 |
|
- turned off sponge layer by default |
1035 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
1036 |
|
- fixed about 35 bugs in obcs_external_fields_load |
1037 |
|
|
1038 |
|
checkpoint55c_post |
1039 |
|
o obcs stuff |
1040 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
1041 |
|
- re-arranged obcs_calc |
1042 |
|
- moved exf_getobcs to obcs_prescibe_read |
1043 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
1044 |
|
and independent of it (executable can contain all). |
1045 |
|
- updated obcs_check |
1046 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
1047 |
|
These may be necessary only if tangential velocities are |
1048 |
|
prescribed at OB, not sure, needs testing. |
1049 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
1050 |
|
which simplifies the calls and passes the ifc check-bounds test |
1051 |
|
|
1052 |
|
checkpoint55b_post |
1053 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
1054 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
1055 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
1056 |
|
affects advect_cs results (for the wrong reason): update output.txt |
1057 |
|
o use a more standard discretization for biharmonic viscosity ; |
1058 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
1059 |
|
affects results of dome set-up: update output.txt |
1060 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
1061 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
1062 |
|
|
1063 |
|
checkpoint55a_post |
1064 |
|
o merged code to |
1065 |
|
* prescribe/read time-dependent open boundaries |
1066 |
|
(works in conjunction with exf, cal) |
1067 |
|
* sponge layer code for open boundaries |
1068 |
|
* each boundary N/S/E/W now has its own CPP option |
1069 |
|
(healthy for the adjoint) |
1070 |
|
|
1071 |
|
checkpoint55 |
1072 |
|
o up-to-date adjoint of previous breaks |
1073 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
1074 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
1075 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
1076 |
|
- carbon: * remove tr1-related adjoint verification |
1077 |
|
* add ptracer as control variable |
1078 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
1079 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
1080 |
|
|
1081 |
|
checkpoint54f_post |
1082 |
|
o in verification/carbin/ remove experiment related to |
1083 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
1084 |
|
code_ad/ input_ad/ results_ad |
1085 |
|
|
1086 |
|
o add two new packages |
1087 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
1088 |
|
+ subject to optimization (memory) |
1089 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
1090 |
|
+ subject to reordering (many GOTOs in the original code) |
1091 |
|
+ so far opps is called for every (i,j) point, and then operates in |
1092 |
|
the vertical; one may want to reorder the scheme in order operate in |
1093 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
1094 |
|
fields) |
1095 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
1096 |
|
- all verification tests compile and run with linux_ia32_g77 |
1097 |
|
- defaults are compatible with current input files--nothing |
1098 |
|
should change if you were not previously using MNC |
1099 |
|
- MNC output has been added in numerous places (eg. timeave) |
1100 |
|
but there are still a few writes not yet do-able with MNC |
1101 |
|
(this is in progress) |
1102 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
1103 |
|
documentation will soon follow |
1104 |
|
- numerous small formatting cleanups for ProTeX |
1105 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
1106 |
|
|
1107 |
|
checkpoint54e_post |
1108 |
|
o add two new packages |
1109 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
1110 |
|
stratification dependent mixing |
1111 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
1112 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
1113 |
|
course), however there is only one diffusivity that is used for both |
1114 |
|
temperature and salinity (and passive tracers)ç |
1115 |
|
o add offline package |
1116 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
1117 |
|
provided by Stephanie Dutkiewicz |
1118 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
1119 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
1120 |
|
|
1121 |
|
checkpoint54d_post |
1122 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
1123 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
1124 |
|
leading to additional shift by 5 days each year of integration |
1125 |
|
(i.e. leading to considerable offset over the years) |
1126 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
1127 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
1128 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
1129 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
1130 |
|
(external loading & cpl import/export stay in forward_step.F) |
1131 |
|
o update coupling interface to work with new staggerTimeStep |
1132 |
|
o change MDSIO ptracers_pickup. |
1133 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
1134 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
1135 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
1136 |
|
|
1137 |
|
checkpoint54c_post |
1138 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
1139 |
|
this affects (truncation error) output.txt of test-exp: |
1140 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
1141 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
1142 |
|
o change Qnet to always be the net heat flux, (+upward). |
1143 |
|
affects (truncation error) output of natl_box exp.: updated |
1144 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
1145 |
|
o start to test mnc routinely in exp0 |
1146 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
1147 |
|
|
1148 |
|
checkpoint54b_post |
1149 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
1150 |
|
impressive on Altix and Opteron systems) |
1151 |
|
o diagnostics can now write NetCDF files through the mnc package |
1152 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
1153 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
1154 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
1155 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
1156 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
1157 |
|
|
1158 |
|
checkpoint54a_post |
1159 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
1160 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
1161 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
1162 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
1163 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
1164 |
|
checkpoint54a_pre |
1165 |
|
|
1166 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
1167 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
1168 |
|
|
1169 |
|
checkpoint54 |
1170 |
|
checkpoint53g_post |
1171 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
1172 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
1173 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
1174 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
1175 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
1176 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
1177 |
|
o restore adjointability |
1178 |
|
|
1179 |
|
checkpoint53f_post |
1180 |
|
o modifications that affect AIM experiment results (update output.txt): |
1181 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
1182 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
1183 |
|
o AIM pkg: |
1184 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
1185 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
1186 |
|
|
1187 |
|
checkpoint53e_post |
1188 |
|
o merged cylindrical coord configuration |
1189 |
|
o added rotating_tank experiment |
1190 |
|
checkpoint53e_pre |
1191 |
|
|
1192 |
|
checkpoint53d_post |
1193 |
|
o faulks upgraded: re-generate output.txt that have changed: |
1194 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
1195 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
1196 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
1197 |
|
o added Sadourny discretization of Coriolis |
1198 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
1199 |
|
- re-enabled use of omega3 (useAbsVorticity) |
1200 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
1201 |
|
vector-invariant equations |
1202 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
1203 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
1204 |
|
hopefully without new bugs |
1205 |
|
- still to do: biharmonic friction for non-hydrostatic w |
1206 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
1207 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
1208 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
1209 |
|
of mom_common/ |
1210 |
|
- simple re-arrangement of instructions within computing loop |
1211 |
|
checkpoint53d_pre |
1212 |
|
|
1213 |
|
checkpoint53c_post |
1214 |
|
o new version of coupler for AIM+thSIce and Ocean models |
1215 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
1216 |
|
- land: change Evaporation of snow |
1217 |
|
- aim with thSIce: fix bug in snow-precip. |
1218 |
|
o changes to calc_gw.F |
1219 |
|
- bug fix for w^2 term near the bottom boundary |
1220 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
1221 |
|
partial/looped cells |
1222 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
1223 |
|
and plume on slope), change the lateral boundary condition from half slip |
1224 |
|
to the value of no_slip_sides |
1225 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
1226 |
|
o Adjoint of EBM package + verification |
1227 |
|
* TLM OK |
1228 |
|
* ADM not sufficient accuracy yet (needs further testing) |
1229 |
|
|
1230 |
|
checkpoint53b_post |
1231 |
|
o Commiting new energy balance model to repository |
1232 |
|
* package is pkg/ebm |
1233 |
|
* verif. is verification/global_ocean_ebm |
1234 |
|
* references are in ebm_driver.F |
1235 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
1236 |
|
C Global thermohaline circulation. Part I: |
1237 |
|
C Sensitivity to atmospheric moisture transport. |
1238 |
|
C J. Climate 12(1), 71-82 |
1239 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
1240 |
|
C Global thermohaline circulation. Part II: |
1241 |
|
C Sensitivity with interactive transport. |
1242 |
|
C J. Climate 12(1), 83-91 |
1243 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
1244 |
|
C Destabilization of the thermohaline circulation |
1245 |
|
C by atmospheric eddy transports. |
1246 |
|
C J. Climate 7(12), 1870-1882 |
1247 |
|
o Will need long integration testing. |
1248 |
|
checkpoint53b_pre |
1249 |
|
|
1250 |
|
o created pkg/mom_common in preparation for variable viscosity code |
1251 |
|
o renamed and split ini_mnc_io |
1252 |
|
o pkg/land: only liquid water can diffuse or run-off |
1253 |
|
o AIM using land: soil wetness availability account for snow |
1254 |
|
o added printMapIncludesZeros to EEPARMS namelist |
1255 |
|
|
1256 |
|
checkpoint53a_post |
1257 |
|
o restore TAMC compatiility for exf_constants.h |
1258 |
|
(no usage of _d in .h) |
1259 |
|
o Additional storing in KPP in an attempt to fix |
1260 |
|
TAMC problem with adjoint of KPP code. |
1261 |
|
(no success...) |
1262 |
|
Identical code works fine with TAF. |
1263 |
|
o Fixed verification/natl_box_adjoint experiments. |
1264 |
|
Initial conditions for Experiments 4 and 5 are now |
1265 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
1266 |
|
and hence gives results closer to that of Experiment 2. |
1267 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
1268 |
|
|
1269 |
|
checkpoint53 |
1270 |
|
o stable checkpoint with up to date adjoint |
1271 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
1272 |
|
this is a code problem or a problem with resetting code for g_ |
1273 |
|
variables that is being autogenerated wrong. |
1274 |
|
Otherwise: |
1275 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
1276 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
1277 |
|
are both still in chaos following their security messes. |
1278 |
|
|
1279 |
|
checkpoint52n_post |
1280 |
|
o various build (mostly genmake2) changes including: |
1281 |
|
- ability to build/run more easily within Cygwin and MacOS X |
1282 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
1283 |
|
o pkg/seaice modifications |
1284 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
1285 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
1286 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
1287 |
|
- changed proxy for geostrophic velocity and updated |
1288 |
|
verification/lab_sea/results/* accordingly |
1289 |
|
- removed ADI dynamic solver from pkg/seaice |
1290 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
1291 |
|
they caused a segmentation fault under certain circumstances |
1292 |
|
- removed unused field WATR |
1293 |
|
o bug fix in exf-package: |
1294 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
1295 |
|
now reflect that. |
1296 |
|
o small fixes in the cal-package: |
1297 |
|
- set reference date to first of January for the 'model'-calendar |
1298 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
1299 |
|
warning |
1300 |
|
o small modifications in exf-package to increase flexibility: |
1301 |
|
- change climtempfreeze from a constant to a runtime parameter that |
1302 |
|
is specified in data.exf_clim (default = -1.9) |
1303 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
1304 |
|
specified in data.exf |
1305 |
|
o fix in pkg/thsice: |
1306 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
1307 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
1308 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
1309 |
|
|
1310 |
|
checkpoint52m_post |
1311 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
1312 |
|
this does not change any of the results, because myIter=0 in swfrac always |
1313 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
1314 |
|
as a default |
1315 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
1316 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
1317 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
1318 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
1319 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
1320 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
1321 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
1322 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
1323 |
|
o monitor package can write to NetCDF files and/or STDOUT |
1324 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
1325 |
|
o doc/api_reference added |
1326 |
|
- a framework for building an API Reference Manual using all |
1327 |
|
the "protex" comments embedded in the code |
1328 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
1329 |
|
o MNC: |
1330 |
|
- make myThid the last argument for all subroutines |
1331 |
|
- new default for the grid files: NO halos |
1332 |
|
- add useMNC and other run-time flags |
1333 |
|
- separate per-file-group handling of the unlimited dimension |
1334 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
1335 |
|
and lookup tables set in initialize_fixed |
1336 |
|
- write all MNC output to a freshly-created directory |
1337 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
1338 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
1339 |
|
o Added functionality to grdchk: |
1340 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
1341 |
|
|
1342 |
|
checkpoint52l_post |
1343 |
|
o new land formulation: |
1344 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
1345 |
|
energy conservation. |
1346 |
|
b) account for water temperature and for latent heat of freezing |
1347 |
|
in all processes (rain, run-off, ground storage) |
1348 |
|
c) compute surface and ground temperature implicitly. |
1349 |
|
o aim_v23 modification for new land model: |
1350 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
1351 |
|
to allow implicit computation of land & sea-ice surface temp. |
1352 |
|
b) add snow precipitation. |
1353 |
|
checkpoint52l_pre |
1354 |
|
|
1355 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
1356 |
|
o fix bug in timeAve (u,vZetatave in common block) |
1357 |
|
o no restoring terms under ice for pkg/seaice |
1358 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
1359 |
|
o bug fix for pkg/seaice pickups |
1360 |
|
o change MNC call locations and add coordinate attributes |
1361 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
1362 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
1363 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
1364 |
|
o exf: Adding simple range check routine for exf fields after read |
1365 |
|
|
1366 |
|
checkpoint52k_post |
1367 |
|
o removed top-level directory "diags" |
1368 |
|
- we migrated these functions to pkg/timeave a long time ago |
1369 |
|
o fixed bug introduced in pkg/monitor |
1370 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
1371 |
|
averaged fields (I/O via cost_averages) |
1372 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
1373 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
1374 |
|
o added initial do_the_model_io to ecco |
1375 |
|
o set all ...Freq to zero after cost_final |
1376 |
|
taveFreq, dumpFreq, pChkptFreq |
1377 |
|
o MAIN and ECCO differentiability restored |
1378 |
|
|
1379 |
|
checkpoint52j_post |
1380 |
|
o fix nchklev in tamc.h for global_ocean... |
1381 |
|
o Bringing flow and store directives up-to-date |
1382 |
|
o Really weird thing! |
1383 |
|
call do_the_model_io from the_main_loop with parameters |
1384 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
1385 |
|
TAF places a faulty re-call of initialise_varia |
1386 |
|
after cost_final call which should not be there! |
1387 |
|
checkpoint52j_pre |
1388 |
|
|
1389 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
1390 |
|
error messages |
1391 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
1392 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
1393 |
|
debug output |
1394 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
1395 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
1396 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
1397 |
|
o update AIM Equatorial Channel exp: |
1398 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
1399 |
o globalFile now works with exch2 |
o globalFile now works with exch2 |
1400 |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
1401 |
mon_vort3.F to make exch2 friendly with >1 tile per cube |
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
1402 |
face |
o limit timeave output for hi-res integrations |
1403 |
|
|
1404 |
checkpoint52i_post |
checkpoint52i_post |
1405 |
o removed CPP_EEOPTIONS.h from verification/*/code |
o removed CPP_EEOPTIONS.h from verification/*/code |