1 |
$Header$ |
$Header$ |
2 |
|
$Name$ |
3 |
|
|
4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
8 |
|
|
9 |
|
checkpoint58j_post |
10 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
11 |
|
from file (collects calls previously in FORWARD_STEP) |
12 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
13 |
|
o adjoint store dir. adjusted accordingly |
14 |
|
o genmake2 |
15 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
16 |
|
|
17 |
|
checkpoint58i_post |
18 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
19 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
20 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
21 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
22 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
23 |
|
on CS-grid: no longer loosing mass. |
24 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
25 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
26 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
27 |
|
- Set to false in order to start EVP solver with |
28 |
|
non-EVP pickup files when using SEAICEuseEVP |
29 |
|
- fix sign error in diffusion in seaice_calc_rhs |
30 |
|
|
31 |
|
checkpoint58h_post |
32 |
|
* Modifications for bottom topography control |
33 |
|
o replace hFacC by _hFacC at various places |
34 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
35 |
|
o add non-self-adjoint cg2d_nsa |
36 |
|
o update autodiff support routines |
37 |
|
o re-initialise hfac after ctrl_depth_ini |
38 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
39 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
40 |
|
|
41 |
|
checkpoint58g_post |
42 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
43 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
44 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
45 |
|
o pkg/ggl90: |
46 |
|
- add parameter (minimum surface kinetic energy) |
47 |
|
- fix bug (avoiding division by zero) |
48 |
|
o couple pkg/thsice to pkg/seaice: |
49 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
50 |
|
- only muliDimAdection scheme work with seaice/thsice |
51 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
52 |
|
- does not break the verification experiments, but does not give the |
53 |
|
desired results either |
54 |
|
o pkg/seaice |
55 |
|
- make (default) second order advection a bit less confusing? |
56 |
|
|
57 |
|
checkpoint58f_post |
58 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
59 |
|
to pkg/seaice): |
60 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
61 |
|
- add an additional formal parameter to thsice_solve4temp |
62 |
|
o pkg/exf: |
63 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
64 |
|
- correct Stefan-Boltzmann constant |
65 |
|
- new parameter for longwave surface emittance |
66 |
|
- separate some stuff from exf_bulkformulae into new routines |
67 |
|
exf_radiation, exf_wind |
68 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
69 |
|
and snow, evaporation parameters over ice |
70 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
71 |
|
either wind from stress or stress from wind |
72 |
|
o pkg/thSIce: |
73 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
74 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
75 |
|
and THSICE_CALC_THICKN |
76 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
77 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
78 |
|
to make debugging easier. |
79 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
80 |
|
o pkg/bulk_force: |
81 |
|
- clean-up comments and parameters ; |
82 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
83 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
84 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
85 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
86 |
|
testreport accordingly |
87 |
|
|
88 |
|
checkpoint58e_post |
89 |
|
o SEAICE_CGRID adjoint done |
90 |
|
o R_STAR adjoint implemented. |
91 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
92 |
|
* need to sort out init. of h0facc, etc. |
93 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
94 |
|
to be able to use it in pure forward. |
95 |
|
|
96 |
|
checkpoint58d_post |
97 |
|
o upgrade simple test-experiment to tutorial example: |
98 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
99 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
100 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
101 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
102 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
103 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
104 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
105 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
106 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
107 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
108 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
109 |
|
o correct a sign problem in cost_scat.F |
110 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
111 |
|
with larger stencil |
112 |
|
o thsice adjoint: start |
113 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
114 |
|
completeness |
115 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
116 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
117 |
|
o ptracers adjoint: |
118 |
|
* avoid extensive recomputatations |
119 |
|
* fix missing re-init. of gptr (missed by TAF) |
120 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
121 |
|
me to turn off the excessive output to STDOUT that this package produces |
122 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
123 |
|
and add those terms in Vector-Invariant formulation. |
124 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
125 |
|
if the control period (xx_hfluxperiod etc) is 0 |
126 |
|
o in profiles pkg, clean routines and fix details |
127 |
|
o in ecco pkg, reading ssh data: |
128 |
|
fix problem in case the model does not start at iter0=0 |
129 |
|
o fix mnc-pickup/restart for ptracers |
130 |
|
o new package prifiles: |
131 |
|
code to compute profile-based cost by Gael Forget |
132 |
|
(modifs in ecco, ctrl, autodiff) |
133 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
134 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
135 |
|
|
136 |
|
checkpoint58c_post |
137 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
138 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
139 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
140 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
141 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
142 |
|
with SEAICE_CGRID defined. |
143 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
144 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
145 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
146 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
147 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
148 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
149 |
|
o fix bug in quasihydrostatic S/R ; |
150 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
151 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
152 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
153 |
|
o add on/off flag useOffLine for package OFFLINE |
154 |
|
o seaice: |
155 |
|
- modify advection so that it works also on the C-grid |
156 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
157 |
|
problem in multi-tile runs with C-grid |
158 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
159 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
160 |
|
C-grid solver |
161 |
|
- added a few comments to seaice_diffusion.F |
162 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
163 |
|
are now exclusive) |
164 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
165 |
|
required re-ordering the code a little: |
166 |
|
+ make DAIRN global variable (defined in SEAICE) |
167 |
|
+ move computation of the viscosities eta and zeta into a new separate |
168 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
169 |
|
|
170 |
|
checkpoint58b_post |
171 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
172 |
|
update output.txt of exp. aim.5l_cs.thSI |
173 |
|
o various mnc cleanups and improvements: |
174 |
|
+ shrink lookup tables by factor of ~4 |
175 |
|
+ better error reporting when running out of lookup space |
176 |
|
+ able to handle longer path/file names (up to 500 chars) |
177 |
|
o adjoint: |
178 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
179 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
180 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
181 |
|
(allow to differentiate between forcing components using new integer flags: |
182 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
183 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
184 |
|
o ecco |
185 |
|
- enable trend removal from SSH anomaly obs. |
186 |
|
o adjoint |
187 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
188 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
189 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
190 |
|
(NLFS seems broken sometimes after I checked it in) |
191 |
|
o seaice: |
192 |
|
- add c-grid version of the dynamic solver: |
193 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
194 |
|
and ostres |
195 |
|
+ put a few fields that were local to dynsolver into global common |
196 |
|
blocks, so that I can move the computation of stresses etc into |
197 |
|
seaice_lsr (saves coding but may break the adjoint). |
198 |
|
- replace more hardwired parameters by runtime parameters |
199 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
200 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
201 |
|
if this works properly), eventually this should replace the clipping |
202 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
203 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
204 |
|
include it only where its needed |
205 |
|
o move balancing of fluxes before the call of external_forcing_surf |
206 |
|
o seaice: |
207 |
|
- correct units of turning angles (now they are really in degrees) |
208 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
209 |
|
- initialize GWATX/Y in seaice_init |
210 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
211 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
212 |
|
o seaice: add runtime flags for turning angles (default to zero) |
213 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
214 |
|
and trend from exf forcing and ctrl control adjustments |
215 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
216 |
|
(since checkpoint57x_post) |
217 |
|
o change the default rotation period to 86164.s = the Earth rotation |
218 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
219 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
220 |
|
o seaice advection: add code for choosing between the default (2nd order |
221 |
|
central differences) and multiDim advection schemes provided by |
222 |
|
pkg/generic_advdiff |
223 |
|
o seaice: |
224 |
|
- removed all references to SEAICE_GRID.h fields from |
225 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
226 |
|
(cubed-sphere configuration will change a little) |
227 |
|
- grid computations in seaice_init are obsolete now. |
228 |
|
- cleaned up code a little so that is easier to read (hopefully). |
229 |
|
- added new (better?) discretizations of default advection and diffusion |
230 |
|
(turn on with SEAICEuseFluxForm) |
231 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
232 |
|
|
233 |
|
checkpoint58a_post |
234 |
|
o seaice: |
235 |
|
- bug fix in advect.F |
236 |
|
o shelfice: |
237 |
|
- separate shelfice load anomaly from pload (breaks with time |
238 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
239 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
240 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
241 |
|
done offline. A good approximation of the pressure load anomaly is |
242 |
|
necessary to avoid large initial adjustment processes underneath |
243 |
|
deep-reaching shelfice. |
244 |
|
- small fix in ISOMIP shelfice_thermodynamics |
245 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
246 |
|
now the default |
247 |
|
- give a few constants more intuitive names |
248 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
249 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
250 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
251 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
252 |
|
STDOUT. |
253 |
|
o fix bug (typo) in obcs_apply_eta.F |
254 |
|
o add a new package shelfice which enables us to model the circulation |
255 |
|
underneath shelf-ice with draughts of hundreds of meters. |
256 |
|
- works |
257 |
|
- to do: + include improved thermodynamics |
258 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
259 |
|
instead of new field kTopC |
260 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
261 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
262 |
|
and ini_mask_etc.F? |
263 |
|
+ adjust vertical mixing schemes? |
264 |
|
o seaice pkg: |
265 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
266 |
|
freezing point of sea water at the surface |
267 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
268 |
|
meridional stresses are now different (and hopefully correct) |
269 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
270 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
271 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
272 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
273 |
|
diagnostics ; define regions by reading a region-mask from a file |
274 |
|
(might add other options later) |
275 |
|
o pkg/bulk_force: |
276 |
|
- add option and parameters to use AIM surface-flux formulae. |
277 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
278 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
279 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
280 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
281 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
282 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
283 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
284 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
285 |
|
|
286 |
|
checkpoint58 |
287 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
288 |
|
tools can be compiled (as determined by genmake2) will turn on the |
289 |
|
embed_files package which then embeds the entire MITgcm source code |
290 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
291 |
|
- requested by CNH but off by default |
292 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
293 |
|
- only writes the output when useEMBEDSRC in eedata is true |
294 |
|
o clean up 3-dim. relaxation codes: |
295 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
296 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
297 |
|
* Thanks to Tom Haine for testing! |
298 |
|
|
299 |
|
checkpoint57z_post |
300 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
301 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
302 |
|
o fix the pickup behavior for obcs in combination with ptracers |
303 |
|
o fix a bug in ptracers_external_fields_load |
304 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
305 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
306 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
307 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
308 |
|
and update lab_sea output.txt file. |
309 |
|
o completing 3-dim. relaxation code: additional term |
310 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
311 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
312 |
|
* At compile time, in "EXF_OPTIONS.h" set |
313 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
314 |
|
#define ALLOW_CLIMSALT_RELAXATION |
315 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
316 |
|
tauThetaClimRelax3Dim = 15552000.0, |
317 |
|
tauSaltClimRelax3Dim = 15552000.0, |
318 |
|
* 3 cases: |
319 |
|
1) Use a constant-in-time 3-dim. field |
320 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
321 |
|
3) Real-time relax. to time-evolving prescribed field |
322 |
|
o Adding Laplacian-type smoothness constraint on |
323 |
|
initial and boundary (forcing) controls (ic, bc) |
324 |
|
* enable at compile-time via |
325 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
326 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
327 |
|
* Absolute scale somewhat unclear so far |
328 |
|
* no area weighting was included since no other cost term does so far |
329 |
|
|
330 |
|
checkpoint57y_post |
331 |
|
First step for a NLFS adjoint |
332 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
333 |
|
o new init. routines for calc_r_star, calc_surf_dr |
334 |
|
o still need to deal with ini_masks_etc |
335 |
|
o testreport seemed happy |
336 |
|
checkpoint57y_pre |
337 |
|
|
338 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
339 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
340 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
341 |
|
o cfc fixes for final year of integration |
342 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
343 |
|
be in GCHEM_OPTIONS). |
344 |
|
|
345 |
|
checkpoint57x_post |
346 |
|
o fix testreport Pb in multiple test experiment. |
347 |
|
o cleanup our namelist syntax in verification: |
348 |
|
- make it more F95 standards compliant (some work still needed) |
349 |
|
- allows the vast majority of our tests to work with gfortran |
350 |
|
o Non-Hydrostatic: |
351 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
352 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
353 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
354 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
355 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
356 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
357 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
358 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
359 |
|
o remove some unused variables (reduces number of compiler warnings) |
360 |
|
o adjoint |
361 |
|
* Disable useVariableViscosity for adjoint for time being |
362 |
|
(there are a number of extensive recomputations) |
363 |
|
* Initialize certain variables needed for adjoint |
364 |
|
|
365 |
|
checkpoint57w_post |
366 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
367 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
368 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
369 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
370 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
371 |
|
o tracer advection scheme: |
372 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
373 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
374 |
|
was not very convenient). |
375 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
376 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
377 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
378 |
|
and sRef for convenience, handy, when you want to initialize |
379 |
|
ptracers in a large domain with a constant non-zero value. Also, |
380 |
|
untangle ptracers_init.F a little. |
381 |
|
|
382 |
|
checkpoint57v_post |
383 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
384 |
|
o remove all the files from the cfc_offline test since they are now |
385 |
|
incorporated into tutorial_cfc_offline which has been producing |
386 |
|
identical results for a few days of testing |
387 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
388 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
389 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
390 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
391 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
392 |
|
o vorticity & strain are now computed without masking, to account for |
393 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
394 |
|
anyway later on, before computing advection/coriolis terms. |
395 |
|
o modify exp4 to test new obcs support for reading from external files |
396 |
|
and for passive tracers |
397 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
398 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
399 |
|
file). |
400 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
401 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
402 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
403 |
|
to be proportional to enstrophy dissipation length. Thus, |
404 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
405 |
|
This is now consistent with Smagorinsky and with the manual. |
406 |
|
|
407 |
|
checkpoint57u_post |
408 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
409 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
410 |
|
OB-values from file; this is not different from the way theta and salinity |
411 |
|
are treated |
412 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
413 |
|
will stop if you use pTracers and Orlanski at the same time. |
414 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
415 |
|
boundary values are overwritten with values from files for which there |
416 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
417 |
|
it possible to use different OBs at different ends of the domain (as |
418 |
|
with EXF) |
419 |
|
o reduce number of exch calls in shap_filt (s2). |
420 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
421 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
422 |
|
|
423 |
|
checkpoint57t_post |
424 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
425 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
426 |
|
same truncation, independent of the face number: affects affects several |
427 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
428 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
429 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
430 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
431 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
432 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
433 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
434 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
435 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
436 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
437 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
438 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
439 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
440 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
441 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
442 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
443 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
444 |
|
Many new viscosity diagnostics available. |
445 |
|
|
446 |
|
checkpoint57s_post |
447 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
448 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
449 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
450 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
451 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
452 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
453 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
454 |
|
ViscAhStrain and viscAhTension are now retired. |
455 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
456 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
457 |
|
that it finds in the *current* directory when searching for files. |
458 |
|
Soft-links found in any other source directories will still work as |
459 |
|
they did before. |
460 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
461 |
|
a C routine to unlimit the stack size |
462 |
|
o mnc-ify pkg/aim snapshot vars |
463 |
|
o mnc-ify pkg/land as requested by Daniel |
464 |
|
o various changes to mnc including: |
465 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
466 |
|
- output can now be grouped so that all files within a group |
467 |
|
change the ITER portion of their names in lock-step together |
468 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
469 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
470 |
|
- writing works for all verification test cases w/ g77 on Linux |
471 |
|
|
472 |
|
checkpoint57r_post |
473 |
|
o make MNC variable initialization happen earlier |
474 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
475 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
476 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
477 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
478 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
479 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
480 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
481 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
482 |
|
o add time-dependent SST, SSS control |
483 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
484 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
485 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
486 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
487 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
488 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
489 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
490 |
|
(see README file) |
491 |
|
|
492 |
|
checkpoint57q_post |
493 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
494 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
495 |
|
- bug was reported by Jean-Michel and Ian Fenty |
496 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
497 |
|
update exp. cpl_aim+ocn output. |
498 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
499 |
|
Needed for high-res. runs with large global files |
500 |
|
to be able to limit tapelev size |
501 |
|
o Changed some tests for adjoint: |
502 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
503 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
504 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
505 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
506 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
507 |
|
* converts, compiles and runs successfully; |
508 |
|
|
509 |
|
checkpoint57p_post |
510 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
511 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
512 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
513 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
514 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
515 |
|
(was already the case for dissipation with mom_vecinv, |
516 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
517 |
|
This will allow to put dissipation out-off the AB time-stepping. |
518 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
519 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
520 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
521 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
522 |
|
|
523 |
|
checkpoint57o_post |
524 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
525 |
|
(2) its ready to be documented during the 20050801 DocFest |
526 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
527 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
528 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
529 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
530 |
|
(worth another tag) |
531 |
|
|
532 |
|
checkpoint57n_post |
533 |
|
o adding precip control xx_precip 32 |
534 |
|
o adding swflux control xx_swflux 33 |
535 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
536 |
|
o Implementing partitioning in time-mean and variable adjustment |
537 |
|
for atmos. state. |
538 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
539 |
|
o in natl_box_adjoint: |
540 |
|
* updated exp 1 to 10 |
541 |
|
(but does not have time-mean vs. variable split results yet) |
542 |
|
o updated global1x1/*_seaice_adj/ |
543 |
|
to incorporate latest changes |
544 |
|
o enable useSingleCpuIO for mdsio vector routines |
545 |
|
(applies in particular to tapelev I/O) |
546 |
|
o removed inefficient K-loop in all active_file*control*.F |
547 |
|
|
548 |
|
checkpoint57m_post |
549 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
550 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
551 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
552 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
553 |
|
|
554 |
|
checkpoint57l_post |
555 |
|
tag before updating tutorials (pre-release-2) |
556 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
557 |
|
for output and interpolation of input fields onto model grid) |
558 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
559 |
|
Affects results of exp. rotating_tank ; update output.txt. |
560 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
561 |
|
and taking the square quantity and/or using a fraction-weight field. |
562 |
|
o fix aim_diagnostics_init.F mate numbers. |
563 |
|
o add mnc output capability to diagnostics/diagstat and update |
564 |
|
our cvsignore files for the ACSII output generated |
565 |
|
|
566 |
|
checkpoint57k_post |
567 |
|
o lab_sea now uses diagnostics package and provides a suite of |
568 |
|
new EXF diagnostics output. |
569 |
|
|
570 |
|
checkpoint57j_post |
571 |
|
o exf |
572 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
573 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
574 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
575 |
|
* extended diagnostics output |
576 |
|
- now includes all EXF variables |
577 |
|
- hs, hl moved to common block |
578 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
579 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
580 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
581 |
|
* updated verif. lab_sea, global_with_exf |
582 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
583 |
|
to ensure that diagnostics sees a true EXFqnet |
584 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
585 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
586 |
|
several times with different frequencies. |
587 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
588 |
|
- the monitor--MNC output needs work |
589 |
|
- many attributes need to be added (most are currently blank) |
590 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
591 |
|
- many attributes need to be added (most are currently blank) |
592 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
593 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
594 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
595 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
596 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
597 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
598 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
599 |
|
|
600 |
|
checkpoint57i_post |
601 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
602 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
603 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
604 |
|
add 1rst Order upwind vertical Shear. |
605 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
606 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
607 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
608 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
609 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
610 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
611 |
|
some "_d 0", etc. no effect. |
612 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
613 |
|
separate 'iter' variable for iteration count |
614 |
|
o pkg/diagnostics: |
615 |
|
add new capability: output of Global/Regional & per-level statistics ; |
616 |
|
tested against monitor output (including land & thSIce) on various exp. |
617 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
618 |
|
|
619 |
|
checkpoint57h_done |
620 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
621 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
622 |
|
|
623 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
624 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
625 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
626 |
|
and rename it: DIFFERENT_MULTIPLE |
627 |
|
|
628 |
|
checkpoint57h_post |
629 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
630 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
631 |
|
of Nb of iterations). This requires to change data.diagnostics. |
632 |
|
checkpoint57h_pre |
633 |
|
|
634 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
635 |
|
and mnc_outdir_num are false |
636 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
637 |
|
per-file basis, the file precision [default behavior is unchanged] |
638 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
639 |
|
depth based on a temperature/density criterion |
640 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
641 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
642 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
643 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
644 |
|
not mnc -- this mistake was found by JMC and is now corrected |
645 |
|
|
646 |
|
checkpoint57g_post |
647 |
|
o add Adams-Bashforth 3rd Order time stepping: |
648 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
649 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
650 |
|
checkpoint57g_pre |
651 |
|
|
652 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
653 |
|
(default remains spatially uniform constant based on tau) |
654 |
|
o added new control variables |
655 |
|
* init. uVel, vVel, etanN |
656 |
|
* lambda[Theta,Salt]ClimRelax |
657 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
658 |
|
(suggested by G. Forget) |
659 |
|
|
660 |
|
checkpoint57f_post |
661 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
662 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
663 |
|
account for baseTime shift |
664 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
665 |
|
checkpoint57f_pre |
666 |
|
|
667 |
|
o mnc-ifying the seaice package |
668 |
|
o introduced an alternative length scale calculation for use in the limiting |
669 |
|
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
670 |
|
o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S |
671 |
|
o added modified Leith scheme with viscosity proportional to grad(Hdiv) |
672 |
|
as well as grad(vort3). Made it compatible with both approximate form |
673 |
|
for the cubed sphere and full form of these gradients. Added flag |
674 |
|
useFullLeith to select between approximate and full form. |
675 |
|
o add "d0" in getcon.F to reduce differences between compilers/platforms |
676 |
|
update output.txt of exp. fizhi-gridalt-hs |
677 |
|
o change port_rand funtion to allow to set the seed. |
678 |
|
o fix obscure MNC bug involving conversion between reals and integers |
679 |
|
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
680 |
|
new version is now more standards-compliant |
681 |
|
o adjoint-related modifications |
682 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
683 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
684 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
685 |
|
|
686 |
|
checkpoint57e_post |
687 |
|
o Adding eddy stress controls a la Ferreira et al. |
688 |
|
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
689 |
|
|
690 |
|
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
691 |
|
update output.txt of exp. fizhi-gridalt-hs |
692 |
|
o add more "Z" dimensions and associated coordinate vars to MNC |
693 |
|
o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
694 |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
o parameter calendarDumps: when set, approximate months (30-31 days) and years |
695 |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
696 |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |