4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o add new diagnostics to seaice: advective, diffusive fluxes (only for |
8 |
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multidim-advection, for scheme 2 they are not filled) and transports, |
9 |
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thermodynamic growth rates |
10 |
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o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but |
11 |
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leave input file unchanged. Affects results @ truncation level (cg2d match) |
12 |
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and update output of experiments: lab_sea(6), global_ocean.90x40x15(10), |
13 |
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global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
14 |
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+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
15 |
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Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
16 |
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|
17 |
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checkpoint59h |
18 |
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o pkg/exf: |
19 |
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- improve vectorization by moving if-statement out of loops in |
20 |
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exf_mapfields, exf_radiation |
21 |
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- exf_bulkformulae.F: introduce 2D fields and vectorize code |
22 |
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o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
23 |
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o testreport: |
24 |
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- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
25 |
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monitor & update offline_exf_seaice exp. output. |
26 |
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- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
27 |
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o pkg/seaice: |
28 |
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- bug fix in the evp solver: boundary conditions were affected be |
29 |
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masking of zMax/zMin (changes results) |
30 |
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- minor bug fix in boundary conditions in seaice_calc_strainrates |
31 |
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(changes results for no_slip) |
32 |
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- seaice_lsr.F: make interpolation of eta dependent on boundaries |
33 |
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- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
34 |
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- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
35 |
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stress formulation and no-slip boundary conditions |
36 |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
37 |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
38 |
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o pkg/seaice: a first HSALT time stepping equation has been checked in |
39 |
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o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
40 |
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in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
41 |
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without requiring DO-IF statements |
42 |
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o pkg/thsice: |
43 |
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use continuous power-law function for partition of energy between lateral |
44 |
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melting/freezing and thinning/thickening ; old code using step function |
45 |
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still available with #undef THSICE_FRACEN_POWERLAW |
46 |
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update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
47 |
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o testreport: change AD testing : check against results/output_adm.txt |
48 |
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using same scripts as for forward test. |
49 |
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|
50 |
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checkpoint59g |
51 |
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o adjoint testing: in preparation for changing testreport: |
52 |
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- output format: cost and grad written on separated lines |
53 |
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- ad output results in directory "results" (instead of "results_ad") |
54 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
55 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
56 |
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o pkg/ecco: allow user defined cost function contributions |
57 |
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o testreport: |
58 |
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Allow to choose (per experiment) the list of tested output variables |
59 |
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and the main variable (used to issue a pass/FAIL ) ; |
60 |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
61 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
62 |
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Also modify printing of summary: |
63 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
64 |
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b) echo the list of tested variables in the individual summary.txt of |
65 |
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each experiment. |
66 |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
67 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
68 |
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(but still depend on the tile decompostion of the domain). |
69 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
70 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
71 |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
72 |
|
the solution to the stress coupling issues with the B-grid. |
73 |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
74 |
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remove .cvsignore from input dir. (since testreport no longer run here). |
75 |
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o pkg/thsice: |
76 |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
77 |
|
- fix reshaping of sea-ice just after advection: |
78 |
|
melt all the ice only if ice-volume is too small. |
79 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
80 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
81 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
82 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
83 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
84 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
85 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
86 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
87 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
88 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
89 |
|
-> update output.txt |
90 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
91 |
|
this affects truncation error: -> update output.txt of exp: |
92 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
93 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
94 |
|
|
95 |
|
checkpoint59f |
96 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
97 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
98 |
|
a bounded range (in forward mode) |
99 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
100 |
|
internal parameter controls, completements of implementations |
101 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
102 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
103 |
|
(not seem any difference in testing results). |
104 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
105 |
|
at face corners. |
106 |
|
o pkg/generic_advdiff: |
107 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
108 |
|
loop range indices for computing vertical advection tendency |
109 |
|
and do the calculation in the interior only (no overlap) ; |
110 |
|
for now, only implemented for SOM advection (to save CPU time). |
111 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
112 |
|
o exch2 adjoint |
113 |
|
First set of changes: |
114 |
|
- add exch2 hand-written adjoint templates |
115 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
116 |
|
This will require cleanup in pkg/autodiff/*.F |
117 |
|
(changed routines currently kept separate in verif. code/) |
118 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
119 |
|
that used to hide exch2 or cubed-sphere specific code |
120 |
|
(commented via 'cph-exch2') |
121 |
|
o pkg/seaice |
122 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
123 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
124 |
|
output of global_ocean.cs32x15.thsice . |
125 |
|
|
126 |
|
checkpoint59e |
127 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
128 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
129 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
130 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
131 |
|
(#ifdef ALLOW_SALT_PLUME) |
132 |
|
o gather_2d/scatter_2d: removed halo regions |
133 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
134 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
135 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
136 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
137 |
|
so maybe GM/Redi adjoint is now broken. |
138 |
|
o seaice adjoint |
139 |
|
* add AREA, HEFF, HSNOW as control variable |
140 |
|
(should not change lab_sea results) |
141 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
142 |
|
o pkg/seaice: |
143 |
|
* added computation of saltFlux in seaice_growth; |
144 |
|
For time being, sea ice salinity is assumed constant |
145 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
146 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
147 |
|
defaults to 0.0 in order to maintain backward compatibility. |
148 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
149 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
150 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
151 |
|
heat content used to melt or grow ice |
152 |
|
* commented out cap of HICE: it helps keep ice thinner |
153 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
154 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
155 |
|
|
156 |
|
checkpoint59d |
157 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
158 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
159 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
160 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
161 |
|
and change default value of parameter "GM_Small_Number"; |
162 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
163 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
164 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
165 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
166 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
167 |
|
o pkg/seaice: |
168 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
169 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
170 |
|
changes verification/lab_sea |
171 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
172 |
|
read, understand, and debug. This causes changes at the truncation level. |
173 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
174 |
|
part) of the LSR solver. Changes all LSR results. |
175 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
176 |
|
is initilized with small values - does not change lab_sea results. |
177 |
|
- added HsnowFile initialization capability |
178 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
179 |
|
initialization of pkg/smooth and application to control vector |
180 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
181 |
|
o dependencies: pkg/profiles requires pkg/cal |
182 |
|
o pkg/profiles: |
183 |
|
- added option ALLOW_PROFILES_GENERICGRID |
184 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
185 |
|
that interpolation information (grid points and coefficients) is provided |
186 |
|
within the netcdf input files. |
187 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
188 |
|
that allow you to prepare netcdf input files. |
189 |
|
- also modified: cleaner include statements, cleaner error print statements, |
190 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
191 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
192 |
|
o pkg/seaice: |
193 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
194 |
|
requires a new routine: seaice_diagnostics_fill.F |
195 |
|
- make sure that seaice does not move if not forced (pressure replacement |
196 |
|
method, Hibler and Ip, 1995), changes results |
197 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
198 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
199 |
|
It is turned off by default (=-1.), because it changes the results. |
200 |
|
- make it possible to read AREA from a file, too. |
201 |
|
|
202 |
|
checkpoint59c |
203 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
204 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
205 |
|
o pkg/thsice: |
206 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
207 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
208 |
|
o pkg/obcs: |
209 |
|
- bug fix for balance code |
210 |
|
o pkg/seaice: |
211 |
|
- allow values of SEAICE_elasticParm > 1 |
212 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
213 |
|
to SEAICE_elasticParm |
214 |
|
- make lsr boundary conditions free slip (by default), changes result |
215 |
|
- add code for no slip boundary conditions for lsr |
216 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
217 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
218 |
|
o change calculation of Visbeck K: |
219 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
220 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
221 |
|
clipping or linear tappering. |
222 |
|
- fix vertical averaging (wrong by 1/2 level) |
223 |
|
- leave the old version (but will not be maintained) within |
224 |
|
#ifdef OLD_VISBECK_CALC / #endif |
225 |
|
- update output of exp. ideal_2D_oce |
226 |
|
o change error catch in calc_r_star to improve vectorization |
227 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
228 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
229 |
|
o adjoint: |
230 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
231 |
|
(but with modifs/completions/cleanups) |
232 |
|
Storing is now bundled into large arrays to optimized I/O |
233 |
|
(and second step in cleanup of the_main_loop) |
234 |
|
|
235 |
|
checkpoint59b |
236 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
237 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
238 |
|
o pkg/seaice: |
239 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
240 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
241 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
242 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
243 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
244 |
|
better |
245 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
246 |
|
passive tracer to an Age Tracer) + update output.txt |
247 |
|
o pkg/exf: |
248 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
249 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
250 |
|
for now, in exf_bulk_largeyeager04.F only : |
251 |
|
- change implementation for case where windspeed + 2. components wind-stress |
252 |
|
are read-in. AND use rhoConstFresh to convert evap. |
253 |
|
o pkg/seaice: |
254 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
255 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
256 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
257 |
|
o pkg/exf: |
258 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
259 |
|
EXF_INTERPOLATION: |
260 |
|
- merge global_with_exf/code version of exf_interp_read.F |
261 |
|
to the main code ; |
262 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
263 |
|
reading the file ; Important: This options needs to be defined to recover |
264 |
|
previous code. |
265 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
266 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
267 |
|
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
268 |
|
- change discretisation of evp-solver in order to avoid another exchange |
269 |
|
(changes lab_sea) and clean up a little |
270 |
|
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
271 |
|
help the adjoint (this also changes the results slightly) |
272 |
|
- add a few "_d 0" where they had been missing in seaice_evp.F |
273 |
|
- cleaning up: remove unused seaice_calc_rhs.F |
274 |
|
o pkg/exf: some cleaning-up: |
275 |
|
- change various "constants" into runtime parameters |
276 |
|
- cleaned-up Large&Yeager04 routine which should eventually |
277 |
|
replace exf_bulkformulae.F (changed names of S/R and CPP) |
278 |
|
and merged various ALLOW_ATM_WIND options |
279 |
|
only used with thsice pkg (in thsice_get_exf.F): |
280 |
|
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
281 |
|
which are used when useStabilityFct_overIce=TRUE (= the default) |
282 |
|
- change default values of ice & snow emissivity and scale downward LW |
283 |
|
by ice & snow emissivity. |
284 |
|
o pkg/thsice: |
285 |
|
fix few little problems, in thsice_calc_thickn.F: |
286 |
|
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
287 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
288 |
|
and in thsice_extend.F: |
289 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
290 |
|
- start to form ice as soon as the minimum ice-volume is reachable. |
291 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
292 |
|
and cpl_aim+ocn |
293 |
|
o pkg/kpp |
294 |
|
- move computation of surface related input fields to KPP into a new |
295 |
|
subroutine kpp_forcing_surf.F |
296 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
297 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
298 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
299 |
|
be the best fix) |
300 |
|
o pkg/seaice |
301 |
|
- check for inconsistent evp parameter/cpp-flag combination |
302 |
|
- remove leftover errIO flat for obsolete name list error handling |
303 |
|
o OpenAD |
304 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
305 |
|
|
306 |
|
checkpoint59a |
307 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
308 |
|
o pkg/thsice: rename run-time parameters: |
309 |
|
himin -> hIceMin |
310 |
|
himin0 -> hThinIce |
311 |
|
hihig -> hThickIce |
312 |
|
i0 -> i0swFrac |
313 |
|
transCoef -> bMeltCoef |
314 |
|
frac_energy -> fracMelting |
315 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
316 |
|
with default values (for now) that do not change the results. |
317 |
|
remove old version of thsice vars advection in pkg/seaice. |
318 |
|
o in FFIELDS.h: |
319 |
|
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
320 |
|
- make pLoad & sIceLoad always available (but still only used if |
321 |
|
ATMOSPHERIC_LOADING is #define). |
322 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
323 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
324 |
|
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
325 |
|
are no longer updating the vertical diffusivity array |
326 |
|
(passed as argument) but are (re-) setting those arrays. |
327 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
328 |
|
- change (improve?) discretization of stress computations for both |
329 |
|
cgrid-lsr and evp solver |
330 |
|
- add a new routine to compute strain rates |
331 |
|
- the above changes lab_sea results |
332 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
333 |
|
may follow |
334 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
335 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
336 |
|
(to force the user to pick a time step since there is not "safe" way |
337 |
|
of choosing it) |
338 |
|
- add principal stress diagnostics |
339 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
340 |
|
exchanges and b: exchanges for stress trensor components which we do |
341 |
|
not have. |
342 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
343 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
344 |
|
in all cases) |
345 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
346 |
|
- add myThid to all kpp routines (long overdue) |
347 |
|
|
348 |
|
checkpoint59 |
349 |
|
o pkg/exf: |
350 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
351 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
352 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
353 |
|
add missing cvs Header & Name |
354 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
355 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
356 |
|
- retire many _CLIM routines, and remove data.exf_clim |
357 |
|
+ params moved to data.exf |
358 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
359 |
|
climss?period=0 refers to constant field, |
360 |
|
climss?period=-12 to monthly forcing |
361 |
|
- split up namelists in data.exf |
362 |
|
o pkg/seaice: |
363 |
|
- remove seaice_exch and seaice_exch_uv |
364 |
|
- remove superfluous exchange of theta |
365 |
|
- add myThid to seaice_budget_ocean/ice |
366 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
367 |
|
+ new routine |
368 |
|
+ two new field (taux, tauy for stress over ice) |
369 |
|
+ removed one global field (DAIRN) for C-grid case only |
370 |
|
o pkg/thsise |
371 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
372 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
373 |
|
|
374 |
|
checkpoint58y_post |
375 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
376 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
377 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
378 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
379 |
|
o Added capability for 3D specification of background vertical diffusion |
380 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
381 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
382 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
383 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
384 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
385 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
386 |
|
but: - conserving Mass, Heat & Salt. |
387 |
|
- better when using non-linear advection scheme (not yet fully tested) |
388 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
389 |
|
|
390 |
|
checkpoint58x_post |
391 |
|
o IO option for global-file compact format: |
392 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
393 |
|
- add I/O capability (pkg/mdsio). |
394 |
|
- adapt utils/matlab/rdmds.m to read this format. |
395 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
396 |
|
o shelfice: add a few diagnostics |
397 |
|
|
398 |
|
checkpoint58w_post |
399 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
400 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
401 |
|
(and replace horiVertRatio in NH code). |
402 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
403 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
404 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
405 |
|
directly to drive seaice model (C-grid only) |
406 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
407 |
|
- reintroduce computation of wind from stress, |
408 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
409 |
|
mass points to avoid tau = 0 |
410 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
411 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
412 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
413 |
|
(tested on all testreport mnc output files). |
414 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
415 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
416 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
417 |
|
to all packages |
418 |
|
|
419 |
|
checkpoint58v_post |
420 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
421 |
|
useDynP_inEos_Zc tested. |
422 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
423 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
424 |
|
and portions thereof. See read_cs.txt for description and examples. |
425 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
426 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
427 |
|
following the great-circle arc between those 2 points. |
428 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
429 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
430 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
431 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
432 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
433 |
|
- still needs work (not working with some options ; efficiency to improve) |
434 |
|
and serious testing. |
435 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
436 |
|
advect_xy & advect_xz, respectively. |
437 |
|
|
438 |
|
checkpoint58u_post |
439 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
440 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
441 |
|
o testreport: add option "-skipdir" to skip some test. |
442 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
443 |
|
momentum calculation. |
444 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
445 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
446 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
447 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
448 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
449 |
|
Linear Free surface |
450 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
451 |
|
o pkg/thsice: fix reading mnc-pickups |
452 |
|
|
453 |
|
checkpoint58t_post |
454 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
455 |
|
o pkg/mdsio: |
456 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
457 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
458 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
459 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
460 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
461 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
462 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
463 |
|
informations (variable names, time ...) to meta files. |
464 |
|
- modify rdmds.m to give back the meta file content. |
465 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
466 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
467 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
468 |
|
diagnostic pointer. |
469 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
470 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
471 |
|
o fix multi-category seaice: |
472 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
473 |
|
SEAICE_MULTICATEGORY |
474 |
|
- fix short wave heat flux |
475 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
476 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
477 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
478 |
|
o Initial check-in of lab_sea adjoint |
479 |
|
(very similar to natl_box_adjoint/code_seaice) |
480 |
|
* used C-grid and EVP solver |
481 |
|
* used KPP, GM/Redi |
482 |
|
* uses inAdExact=.TRUE. |
483 |
|
* gradient checks fail for both ADM and TLM |
484 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
485 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
486 |
|
issue is related to forward mismatch between g77 an ifort |
487 |
|
o pkg/seaice: overhaul of thermodynamics |
488 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
489 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
490 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
491 |
|
make them 2D (FICE/QNETO/ ...) |
492 |
|
- remove FO (it is the same as QNETO) |
493 |
|
- introduce a few local fields to avoid modifying external fields such |
494 |
|
as atemp, etc. |
495 |
|
|
496 |
|
checkpoint58s_post |
497 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
498 |
|
changed exf_set_gen.F so that |
499 |
|
genperiod=0 means input file is one time-constant field and |
500 |
|
genperiod=-12 means input file contains 12 monthly means |
501 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
502 |
|
this affects truncation error ; generate new output file for exp. which |
503 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
504 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
505 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
506 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
507 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
508 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
509 |
|
o start implementation of deep-atmosphere and anelastic formulation |
510 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
511 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
512 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
513 |
|
o profiles: fix for multithreaded case |
514 |
|
|
515 |
|
o diagnostics: rename few diags: |
516 |
|
s/'PRESSURE'/'RCENTER '/g |
517 |
|
s/'TICE '/'oceFreez'/g |
518 |
|
s/'TAUX '/'oceTAUX '/g |
519 |
|
s/'TAUY '/'oceTAUY '/g |
520 |
|
s/'SWFLUX '/'oceQsw '/g |
521 |
|
s/DIFx/DFxE/g |
522 |
|
s/DIFy/DFyE/g |
523 |
|
and add few ocean-forcing diagnostics: |
524 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
525 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
526 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
527 |
|
as actual snow thickness. It now refers everywhere to effective snow |
528 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
529 |
|
|
530 |
|
checkpoint58r_post |
531 |
|
o modifications to pkg/seaice/growth.F, which change results of |
532 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
533 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
534 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
535 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
536 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
537 |
|
both are turned off by default and do no change any results |
538 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
539 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
540 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
541 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
542 |
|
in natl_box (affects results @ truncation level: update output.txt) |
543 |
|
o multi-threading and IO: |
544 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
545 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
546 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
547 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
548 |
|
affects the results (but none of the verification test uses this scheme). |
549 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
550 |
|
(will certainly be subject to changes) |
551 |
|
o ctrl: adding new control variables: |
552 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
553 |
|
|
554 |
|
checkpoint58q_post |
555 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
556 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
557 |
|
high_res_cube configuration by 4% on Columbia. |
558 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
559 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
560 |
|
dynamical allocation (seems to work in multi-threaded). |
561 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
562 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
563 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
564 |
|
|
565 |
|
checkpoint58p_post |
566 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
567 |
|
o shelfice: |
568 |
|
- fix a sign error so that no slip at shelfice interface works |
569 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
570 |
|
not mean, that the results are correct, but at least they are numerically |
571 |
|
stable |
572 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
573 |
|
o added adjoint exch routined for all exch*3d* routines |
574 |
|
and updated flow directives |
575 |
|
|
576 |
|
checkpoint58o_post |
577 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
578 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
579 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
580 |
|
and clean-up reading/writing of pickup files. |
581 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
582 |
|
o simplify EXCH interface: |
583 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
584 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
585 |
|
o added the regrid package |
586 |
|
o shelfice: |
587 |
|
- add a simple boundary layer scheme to reduce noise |
588 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
589 |
|
|
590 |
|
checkpoint58n_post |
591 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
592 |
|
local variable (not in common block). |
593 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
594 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
595 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
596 |
|
to work with SingleCpuIO. |
597 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
598 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
599 |
|
o multi-threading and IO: |
600 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
601 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
602 |
|
- barrier before and after reading. |
603 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
604 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
605 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
606 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
607 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
608 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
609 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
610 |
|
|
611 |
|
checkpoint58m_post |
612 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
613 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
614 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
615 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
616 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
617 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
618 |
|
add MITgcm_tutorials (= code + all the tutorials) |
619 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
620 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
621 |
|
o profiles: adding ptracer and ssh |
622 |
|
o testreport: change multi-test output-file name |
623 |
|
(from output.txt.{name} to output.{name}.txt) |
624 |
|
o profiles: now ok for mutli-tiles case |
625 |
|
o seaice: add 4 parameters for different advection schemes for area, |
626 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
627 |
|
is the standard parameter SEAICEadvScheme |
628 |
|
o calc_gw: |
629 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
630 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
631 |
|
of tutorial_plume_on_slope. |
632 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
633 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
634 |
|
update rotating_tank results, but not plume_on_slope (affected at |
635 |
|
truncation level, 11 digits). |
636 |
|
|
637 |
|
checkpoint58l_post |
638 |
|
o calc_gw: |
639 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
640 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
641 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
642 |
|
o commit code to make SST/SSS weights spatially variable |
643 |
|
(based on either variable in-situ or variable initial T/S weights) |
644 |
|
o pkg/ecco: |
645 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
646 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
647 |
|
* cost_averagesflags now returns year indices in addition to day, month |
648 |
|
* sflux balance is performed on annual basis |
649 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
650 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
651 |
|
including separate counting and multipliers |
652 |
|
o pkg/rbcs |
653 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
654 |
|
|
655 |
|
checkpoint58k_post |
656 |
|
o testreport: |
657 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
658 |
|
& running in input) |
659 |
|
- run in dir run (if it exists), in build otherwise. |
660 |
|
- call prepare_run (if input/prepare_run exists) |
661 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
662 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
663 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
664 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
665 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
666 |
|
o pkg/exf/exf_check_range.F |
667 |
|
- add tile index to diagnostics and move stop statement to the very |
668 |
|
end of the routine. |
669 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
670 |
|
define title of isomorphic variables according to the current config. |
671 |
|
o pkg/thsice with pkg/seaice dynamics: |
672 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
673 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
674 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
675 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
676 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
677 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
678 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
679 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
680 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
681 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
682 |
|
o tracer advection: |
683 |
|
- clean-up and simplify calc_common_factors.F |
684 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
685 |
|
advection subroutine (but still not used within DST advection S/R) |
686 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
687 |
|
|
688 |
checkpoint58j_post |
checkpoint58j_post |
689 |
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
690 |
from file (collects calls previously in FORWARD_STEP) |
from file (collects calls previously in FORWARD_STEP) |