4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
|
|
7 |
|
o shelfice: |
8 |
|
- add a simple boundary layer scheme to reduce noise |
9 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
10 |
|
checkpoint58n_post |
11 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
12 |
|
local variable (not in common block). |
13 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
14 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
15 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
16 |
|
to work with SingleCpuIO. |
17 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
18 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
19 |
|
o multi-threading and IO: |
20 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
21 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
22 |
|
- barrier before and after reading. |
23 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
24 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
25 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
26 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
27 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
28 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
29 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
30 |
|
|
31 |
|
checkpoint58m_post |
32 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
33 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
34 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
35 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
36 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
37 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
38 |
|
add MITgcm_tutorials (= code + all the tutorials) |
39 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
40 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
41 |
|
o profiles: adding ptracer and ssh |
42 |
|
o testreport: change multi-test output-file name |
43 |
|
(from output.txt.{name} to output.{name}.txt) |
44 |
|
o profiles: now ok for mutli-tiles case |
45 |
|
o seaice: add 4 parameters for different advection schemes for area, |
46 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
47 |
|
is the standard parameter SEAICEadvScheme |
48 |
|
o calc_gw: |
49 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
50 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
51 |
|
of tutorial_plume_on_slope. |
52 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
53 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
54 |
|
update rotating_tank results, but not plume_on_slope (affected at |
55 |
|
truncation level, 11 digits). |
56 |
|
|
57 |
|
checkpoint58l_post |
58 |
|
o calc_gw: |
59 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
60 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
61 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
62 |
|
o commit code to make SST/SSS weights spatially variable |
63 |
|
(based on either variable in-situ or variable initial T/S weights) |
64 |
|
o pkg/ecco: |
65 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
66 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
67 |
|
* cost_averagesflags now returns year indices in addition to day, month |
68 |
|
* sflux balance is performed on annual basis |
69 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
70 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
71 |
|
including separate counting and multipliers |
72 |
|
o pkg/rbcs |
73 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
74 |
|
|
75 |
|
checkpoint58k_post |
76 |
|
o testreport: |
77 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
78 |
|
& running in input) |
79 |
|
- run in dir run (if it exists), in build otherwise. |
80 |
|
- call prepare_run (if input/prepare_run exists) |
81 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
82 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
83 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
84 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
85 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
86 |
|
o pkg/exf/exf_check_range.F |
87 |
|
- add tile index to diagnostics and move stop statement to the very |
88 |
|
end of the routine. |
89 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
90 |
|
define title of isomorphic variables according to the current config. |
91 |
|
o pkg/thsice with pkg/seaice dynamics: |
92 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
93 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
94 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
95 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
96 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
97 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
98 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
99 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
100 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
101 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
102 |
|
o tracer advection: |
103 |
|
- clean-up and simplify calc_common_factors.F |
104 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
105 |
|
advection subroutine (but still not used within DST advection S/R) |
106 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
107 |
|
|
108 |
|
checkpoint58j_post |
109 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
110 |
|
from file (collects calls previously in FORWARD_STEP) |
111 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
112 |
|
o adjoint store dir. adjusted accordingly |
113 |
|
o genmake2 |
114 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
115 |
|
|
116 |
|
checkpoint58i_post |
117 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
118 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
119 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
120 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
121 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
122 |
|
on CS-grid: no longer loosing mass. |
123 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
124 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
125 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
126 |
|
- Set to false in order to start EVP solver with |
127 |
|
non-EVP pickup files when using SEAICEuseEVP |
128 |
|
- fix sign error in diffusion in seaice_calc_rhs |
129 |
|
|
130 |
|
checkpoint58h_post |
131 |
|
* Modifications for bottom topography control |
132 |
|
o replace hFacC by _hFacC at various places |
133 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
134 |
|
o add non-self-adjoint cg2d_nsa |
135 |
|
o update autodiff support routines |
136 |
|
o re-initialise hfac after ctrl_depth_ini |
137 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
138 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
139 |
|
|
140 |
|
checkpoint58g_post |
141 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
142 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
143 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
144 |
|
o pkg/ggl90: |
145 |
|
- add parameter (minimum surface kinetic energy) |
146 |
|
- fix bug (avoiding division by zero) |
147 |
|
o couple pkg/thsice to pkg/seaice: |
148 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
149 |
|
- only muliDimAdection scheme work with seaice/thsice |
150 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
151 |
|
- does not break the verification experiments, but does not give the |
152 |
|
desired results either |
153 |
|
o pkg/seaice |
154 |
|
- make (default) second order advection a bit less confusing? |
155 |
|
|
156 |
|
checkpoint58f_post |
157 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
158 |
|
to pkg/seaice): |
159 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
160 |
|
- add an additional formal parameter to thsice_solve4temp |
161 |
|
o pkg/exf: |
162 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
163 |
|
- correct Stefan-Boltzmann constant |
164 |
|
- new parameter for longwave surface emittance |
165 |
|
- separate some stuff from exf_bulkformulae into new routines |
166 |
|
exf_radiation, exf_wind |
167 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
168 |
|
and snow, evaporation parameters over ice |
169 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
170 |
|
either wind from stress or stress from wind |
171 |
|
o pkg/thSIce: |
172 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
173 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
174 |
|
and THSICE_CALC_THICKN |
175 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
176 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
177 |
|
to make debugging easier. |
178 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
179 |
|
o pkg/bulk_force: |
180 |
|
- clean-up comments and parameters ; |
181 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
182 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
183 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
184 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
185 |
|
testreport accordingly |
186 |
|
|
187 |
|
checkpoint58e_post |
188 |
|
o SEAICE_CGRID adjoint done |
189 |
|
o R_STAR adjoint implemented. |
190 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
191 |
|
* need to sort out init. of h0facc, etc. |
192 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
193 |
|
to be able to use it in pure forward. |
194 |
|
|
195 |
|
checkpoint58d_post |
196 |
|
o upgrade simple test-experiment to tutorial example: |
197 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
198 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
199 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
200 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
201 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
202 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
203 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
204 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
205 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
206 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
207 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
208 |
|
o correct a sign problem in cost_scat.F |
209 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
210 |
|
with larger stencil |
211 |
|
o thsice adjoint: start |
212 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
213 |
|
completeness |
214 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
215 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
216 |
|
o ptracers adjoint: |
217 |
|
* avoid extensive recomputatations |
218 |
|
* fix missing re-init. of gptr (missed by TAF) |
219 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
220 |
|
me to turn off the excessive output to STDOUT that this package produces |
221 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
222 |
|
and add those terms in Vector-Invariant formulation. |
223 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
224 |
|
if the control period (xx_hfluxperiod etc) is 0 |
225 |
|
o in profiles pkg, clean routines and fix details |
226 |
|
o in ecco pkg, reading ssh data: |
227 |
|
fix problem in case the model does not start at iter0=0 |
228 |
|
o fix mnc-pickup/restart for ptracers |
229 |
|
o new package prifiles: |
230 |
|
code to compute profile-based cost by Gael Forget |
231 |
|
(modifs in ecco, ctrl, autodiff) |
232 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
233 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
234 |
|
|
235 |
|
checkpoint58c_post |
236 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
237 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
238 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
239 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
240 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
241 |
|
with SEAICE_CGRID defined. |
242 |
|
o move calendarDumps from "data" to "data.cal" and clean-up the code |
243 |
|
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
244 |
|
o add useEXF & useCAL flags (for now, set in hard-coded way) |
245 |
|
o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
246 |
|
(were missing in NH mode, and wrong in quasihydrostatic mode). |
247 |
|
waiting for Chris updated version of calc_gw to add those CALLs. |
248 |
|
o fix bug in quasihydrostatic S/R ; |
249 |
|
add a test for this option: global_ocean.90x40x15.qshyd |
250 |
|
o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
251 |
|
(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
252 |
|
o add on/off flag useOffLine for package OFFLINE |
253 |
|
o seaice: |
254 |
|
- modify advection so that it works also on the C-grid |
255 |
|
- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
256 |
|
problem in multi-tile runs with C-grid |
257 |
|
- add flags for clipping ice velocities and/or masking solver forcing |
258 |
|
- fix drag (ocean on ice) formulation and a bug that caused noise in the |
259 |
|
C-grid solver |
260 |
|
- added a few comments to seaice_diffusion.F |
261 |
|
- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
262 |
|
are now exclusive) |
263 |
|
- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
264 |
|
required re-ordering the code a little: |
265 |
|
+ make DAIRN global variable (defined in SEAICE) |
266 |
|
+ move computation of the viscosities eta and zeta into a new separate |
267 |
|
routine (because I need to recompute them in seaice_ocean_stress.F) |
268 |
|
|
269 |
|
checkpoint58b_post |
270 |
|
o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
271 |
|
update output.txt of exp. aim.5l_cs.thSI |
272 |
|
o various mnc cleanups and improvements: |
273 |
|
+ shrink lookup tables by factor of ~4 |
274 |
|
+ better error reporting when running out of lookup space |
275 |
|
+ able to handle longer path/file names (up to 500 chars) |
276 |
|
o adjoint: |
277 |
|
- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
278 |
|
- TBD: "hidden" mom_vecinv recomp. in dynamics |
279 |
|
o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
280 |
|
(allow to differentiate between forcing components using new integer flags: |
281 |
|
momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
282 |
|
and add new flag to put Dissipation tendency out of Adams-Bashforth. |
283 |
|
o ecco |
284 |
|
- enable trend removal from SSH anomaly obs. |
285 |
|
o adjoint |
286 |
|
- a fix for PmEpR when #undef EXACT_CONSERV |
287 |
|
- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
288 |
|
- try to fix "hidden" recomp. in forward_step for NLFS |
289 |
|
(NLFS seems broken sometimes after I checked it in) |
290 |
|
o seaice: |
291 |
|
- add c-grid version of the dynamic solver: |
292 |
|
+ three new routines that are the c-grid substitute lsr, dynsolver |
293 |
|
and ostres |
294 |
|
+ put a few fields that were local to dynsolver into global common |
295 |
|
blocks, so that I can move the computation of stresses etc into |
296 |
|
seaice_lsr (saves coding but may break the adjoint). |
297 |
|
- replace more hardwired parameters by runtime parameters |
298 |
|
- add ice masks that mask the rhs of the implicit solvers where there |
299 |
|
is no ice (commented out in seaice_dynsolver, because i am not sure |
300 |
|
if this works properly), eventually this should replace the clipping |
301 |
|
of ice velocities in seaice_dynsolver to +/-40cm/s. |
302 |
|
o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
303 |
|
include it only where its needed |
304 |
|
o move balancing of fluxes before the call of external_forcing_surf |
305 |
|
o seaice: |
306 |
|
- correct units of turning angles (now they are really in degrees) |
307 |
|
- move computation of GWATX/Y out of main routine into dynsolver |
308 |
|
- initialize GWATX/Y in seaice_init |
309 |
|
o Apply mask on Fresh-Water flux (needed for SSH forcing). |
310 |
|
update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
311 |
|
o seaice: add runtime flags for turning angles (default to zero) |
312 |
|
o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
313 |
|
and trend from exf forcing and ctrl control adjustments |
314 |
|
o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
315 |
|
(since checkpoint57x_post) |
316 |
|
o change the default rotation period to 86164.s = the Earth rotation |
317 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
318 |
|
and based on a reference stratification. Tested within hs94.cs-32x32x5. |
319 |
|
o seaice advection: add code for choosing between the default (2nd order |
320 |
|
central differences) and multiDim advection schemes provided by |
321 |
|
pkg/generic_advdiff |
322 |
|
o seaice: |
323 |
|
- removed all references to SEAICE_GRID.h fields from |
324 |
|
dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
325 |
|
(cubed-sphere configuration will change a little) |
326 |
|
- grid computations in seaice_init are obsolete now. |
327 |
|
- cleaned up code a little so that is easier to read (hopefully). |
328 |
|
- added new (better?) discretizations of default advection and diffusion |
329 |
|
(turn on with SEAICEuseFluxForm) |
330 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
331 |
|
|
332 |
|
checkpoint58a_post |
333 |
|
o seaice: |
334 |
|
- bug fix in advect.F |
335 |
|
o shelfice: |
336 |
|
- separate shelfice load anomaly from pload (breaks with time |
337 |
|
dependent forcing), => introduce constant field shelficeLoadAnomaly. |
338 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
339 |
|
t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
340 |
|
done offline. A good approximation of the pressure load anomaly is |
341 |
|
necessary to avoid large initial adjustment processes underneath |
342 |
|
deep-reaching shelfice. |
343 |
|
- small fix in ISOMIP shelfice_thermodynamics |
344 |
|
- add more sophisticated thermodynamics of Hellmer (1989), this is |
345 |
|
now the default |
346 |
|
- give a few constants more intuitive names |
347 |
|
o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
348 |
|
if bulk formulae are used in long integration (especially EmPmR). Turn |
349 |
|
on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
350 |
|
if balancePrintMean, the imbalance that is substracted is printed to |
351 |
|
STDOUT. |
352 |
|
o fix bug (typo) in obcs_apply_eta.F |
353 |
|
o add a new package shelfice which enables us to model the circulation |
354 |
|
underneath shelf-ice with draughts of hundreds of meters. |
355 |
|
- works |
356 |
|
- to do: + include improved thermodynamics |
357 |
|
+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
358 |
|
instead of new field kTopC |
359 |
|
+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
360 |
|
instead of new field R_shelfIce and new code in ini_depth.F |
361 |
|
and ini_mask_etc.F? |
362 |
|
+ adjust vertical mixing schemes? |
363 |
|
o seaice pkg: |
364 |
|
- add a cpp-flag to include a simple formula for a salinity dependent |
365 |
|
freezing point of sea water at the surface |
366 |
|
- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
367 |
|
meridional stresses are now different (and hopefully correct) |
368 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
369 |
|
update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
370 |
|
and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
371 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
372 |
|
diagnostics ; define regions by reading a region-mask from a file |
373 |
|
(might add other options later) |
374 |
|
o pkg/bulk_force: |
375 |
|
- add option and parameters to use AIM surface-flux formulae. |
376 |
|
- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
377 |
|
others forcing fields (defined in PARM05, parameter file "data") are loaded |
378 |
|
from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
379 |
|
- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
380 |
|
- use the right EXCH call for uwind,vwind (to work on CS-grid). |
381 |
|
- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
382 |
|
and parameters (note: calcWindStress replaces .NOT.readwindstress). |
383 |
|
- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
384 |
|
|
385 |
|
checkpoint58 |
386 |
|
o add "--embed-source" option to genmake2 which, when the supporting |
387 |
|
tools can be compiled (as determined by genmake2) will turn on the |
388 |
|
embed_files package which then embeds the entire MITgcm source code |
389 |
|
(*.[fFhc] + Makefile) used for the build within the executable |
390 |
|
- requested by CNH but off by default |
391 |
|
- adds a paltry <9MB to the mitgcmuv executable in most cases |
392 |
|
- only writes the output when useEMBEDSRC in eedata is true |
393 |
|
o clean up 3-dim. relaxation codes: |
394 |
|
* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
395 |
|
* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
396 |
|
* Thanks to Tom Haine for testing! |
397 |
|
|
398 |
|
checkpoint57z_post |
399 |
|
o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
400 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
401 |
|
o fix the pickup behavior for obcs in combination with ptracers |
402 |
|
o fix a bug in ptracers_external_fields_load |
403 |
|
o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
404 |
|
affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
405 |
|
o transfered surface NH pressure to eta field (if exactConserv). |
406 |
|
o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
407 |
|
and update lab_sea output.txt file. |
408 |
|
o completing 3-dim. relaxation code: additional term |
409 |
|
1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
410 |
|
in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
411 |
|
* At compile time, in "EXF_OPTIONS.h" set |
412 |
|
#define ALLOW_CLIMTEMP_RELAXATION |
413 |
|
#define ALLOW_CLIMSALT_RELAXATION |
414 |
|
* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
415 |
|
tauThetaClimRelax3Dim = 15552000.0, |
416 |
|
tauSaltClimRelax3Dim = 15552000.0, |
417 |
|
* 3 cases: |
418 |
|
1) Use a constant-in-time 3-dim. field |
419 |
|
2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
420 |
|
3) Real-time relax. to time-evolving prescribed field |
421 |
|
o Adding Laplacian-type smoothness constraint on |
422 |
|
initial and boundary (forcing) controls (ic, bc) |
423 |
|
* enable at compile-time via |
424 |
|
ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
425 |
|
* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
426 |
|
* Absolute scale somewhat unclear so far |
427 |
|
* no area weighting was included since no other cost term does so far |
428 |
|
|
429 |
|
checkpoint57y_post |
430 |
|
First step for a NLFS adjoint |
431 |
|
o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
432 |
|
o new init. routines for calc_r_star, calc_surf_dr |
433 |
|
o still need to deal with ini_masks_etc |
434 |
|
o testreport seemed happy |
435 |
|
checkpoint57y_pre |
436 |
|
|
437 |
|
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
438 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
439 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
440 |
|
o cfc fixes for final year of integration |
441 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
442 |
|
be in GCHEM_OPTIONS). |
443 |
|
|
444 |
|
checkpoint57x_post |
445 |
|
o fix testreport Pb in multiple test experiment. |
446 |
|
o cleanup our namelist syntax in verification: |
447 |
|
- make it more F95 standards compliant (some work still needed) |
448 |
|
- allows the vast majority of our tests to work with gfortran |
449 |
|
o Non-Hydrostatic: |
450 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
451 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
452 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
453 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
454 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
455 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
456 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
457 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
458 |
|
o remove some unused variables (reduces number of compiler warnings) |
459 |
|
o adjoint |
460 |
|
* Disable useVariableViscosity for adjoint for time being |
461 |
|
(there are a number of extensive recomputations) |
462 |
|
* Initialize certain variables needed for adjoint |
463 |
|
|
464 |
|
checkpoint57w_post |
465 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
466 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
467 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
468 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
469 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
470 |
|
o tracer advection scheme: |
471 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
472 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
473 |
|
was not very convenient). |
474 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
475 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
476 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
477 |
|
and sRef for convenience, handy, when you want to initialize |
478 |
|
ptracers in a large domain with a constant non-zero value. Also, |
479 |
|
untangle ptracers_init.F a little. |
480 |
|
|
481 |
|
checkpoint57v_post |
482 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
483 |
|
o remove all the files from the cfc_offline test since they are now |
484 |
|
incorporated into tutorial_cfc_offline which has been producing |
485 |
|
identical results for a few days of testing |
486 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
487 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
488 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
489 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
490 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
491 |
|
o vorticity & strain are now computed without masking, to account for |
492 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
493 |
|
anyway later on, before computing advection/coriolis terms. |
494 |
|
o modify exp4 to test new obcs support for reading from external files |
495 |
|
and for passive tracers |
496 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
497 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
498 |
|
file). |
499 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
500 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
501 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
502 |
|
to be proportional to enstrophy dissipation length. Thus, |
503 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
504 |
|
This is now consistent with Smagorinsky and with the manual. |
505 |
|
|
506 |
|
checkpoint57u_post |
507 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
508 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
509 |
|
OB-values from file; this is not different from the way theta and salinity |
510 |
|
are treated |
511 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
512 |
|
will stop if you use pTracers and Orlanski at the same time. |
513 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
514 |
|
boundary values are overwritten with values from files for which there |
515 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
516 |
|
it possible to use different OBs at different ends of the domain (as |
517 |
|
with EXF) |
518 |
|
o reduce number of exch calls in shap_filt (s2). |
519 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
520 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
521 |
|
|
522 |
|
checkpoint57t_post |
523 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
524 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
525 |
|
same truncation, independent of the face number: affects affects several |
526 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
527 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
528 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
529 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
530 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
531 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
532 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
533 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
534 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
535 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
536 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
537 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
538 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
539 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
540 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
541 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
542 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
543 |
|
Many new viscosity diagnostics available. |
544 |
|
|
545 |
|
checkpoint57s_post |
546 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
547 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
548 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
549 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
550 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
551 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
552 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
553 |
|
ViscAhStrain and viscAhTension are now retired. |
554 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
555 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
556 |
|
that it finds in the *current* directory when searching for files. |
557 |
|
Soft-links found in any other source directories will still work as |
558 |
|
they did before. |
559 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
560 |
|
a C routine to unlimit the stack size |
561 |
|
o mnc-ify pkg/aim snapshot vars |
562 |
|
o mnc-ify pkg/land as requested by Daniel |
563 |
|
o various changes to mnc including: |
564 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
565 |
|
- output can now be grouped so that all files within a group |
566 |
|
change the ITER portion of their names in lock-step together |
567 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
568 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
569 |
|
- writing works for all verification test cases w/ g77 on Linux |
570 |
|
|
571 |
|
checkpoint57r_post |
572 |
|
o make MNC variable initialization happen earlier |
573 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
574 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
575 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
576 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
577 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
578 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
579 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
580 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
581 |
|
o add time-dependent SST, SSS control |
582 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
583 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
584 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
585 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
586 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
587 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
588 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
589 |
|
(see README file) |
590 |
|
|
591 |
|
checkpoint57q_post |
592 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
593 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
594 |
|
- bug was reported by Jean-Michel and Ian Fenty |
595 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
596 |
|
update exp. cpl_aim+ocn output. |
597 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
598 |
|
Needed for high-res. runs with large global files |
599 |
|
to be able to limit tapelev size |
600 |
|
o Changed some tests for adjoint: |
601 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
602 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
603 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
604 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
605 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
606 |
|
* converts, compiles and runs successfully; |
607 |
|
|
608 |
|
checkpoint57p_post |
609 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
610 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
611 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
612 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
613 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
614 |
|
(was already the case for dissipation with mom_vecinv, |
615 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
616 |
|
This will allow to put dissipation out-off the AB time-stepping. |
617 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
618 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
619 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
620 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
621 |
|
|
622 |
|
checkpoint57o_post |
623 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
624 |
|
(2) its ready to be documented during the 20050801 DocFest |
625 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
626 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
627 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
628 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
629 |
|
(worth another tag) |
630 |
|
|
631 |
checkpoint57n_post |
checkpoint57n_post |
632 |
o adding precip control xx_precip |
o adding precip control xx_precip 32 |
633 |
o moved ptracer ctrl index 17 -> 32 |
o adding swflux control xx_swflux 33 |
634 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
635 |
|
o Implementing partitioning in time-mean and variable adjustment |
636 |
|
for atmos. state. |
637 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
638 |
|
o in natl_box_adjoint: |
639 |
|
* updated exp 1 to 10 |
640 |
|
(but does not have time-mean vs. variable split results yet) |
641 |
|
o updated global1x1/*_seaice_adj/ |
642 |
|
to incorporate latest changes |
643 |
|
o enable useSingleCpuIO for mdsio vector routines |
644 |
|
(applies in particular to tapelev I/O) |
645 |
|
o removed inefficient K-loop in all active_file*control*.F |
646 |
|
|
647 |
checkpoint57m_post |
checkpoint57m_post |
648 |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |