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 Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
8 |
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vertical diffusivity, similar to that in MOM4; vertical diffusivity is |
9 |
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specified using diffKrBL79* diffKrBLEQ* and KbryanLewisLatTransition |
10 |
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o Added capability for 3D specification of background vertical diffusion |
11 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
12 |
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in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
13 |
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"data" file that contains the 3D vertical diffusivity coefficients. |
14 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
15 |
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- add code within pkg thsice to advect & diffuse sea-ice fields |
16 |
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similar to (and will replace) what has been added in seaice_advdiff.F, |
17 |
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but: - conserving Mass, Heat & Salt. |
18 |
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- better when using non-linear advection scheme (not yet fully tested) |
19 |
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- can also be used in atmospheric set-up (for now, only the diffusion). |
20 |
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|
21 |
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checkpoint58x_post |
22 |
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o IO option for global-file compact format: |
23 |
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- add options when generating topology (utils/exch2/matlab-topology-generator) |
24 |
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- add I/O capability (pkg/mdsio). |
25 |
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- adapt utils/matlab/rdmds.m to read this format. |
26 |
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for now long-line format not yet supported by pkg/mdsio (& exch2). |
27 |
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o shelfice: add a few diagnostics |
28 |
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|
29 |
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checkpoint58w_post |
30 |
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o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
31 |
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rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
32 |
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(and replace horiVertRatio in NH code). |
33 |
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Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
34 |
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and tutorial_plume_on_slope (sensitive to truncation) |
35 |
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o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
36 |
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directly to drive seaice model (C-grid only) |
37 |
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o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
38 |
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- reintroduce computation of wind from stress, |
39 |
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- compute tau (in exf_bulkformulae.F) from windstress averaged to |
40 |
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mass points to avoid tau = 0 |
41 |
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- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
42 |
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o rdmnc.m: make it work with "global" files created with gluemnc |
43 |
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o rdmnc.m : some improvements in dealing with singleton dimension |
44 |
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(tested on all testreport mnc output files). |
45 |
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o genmake2: disable pkg/profiles if netcdf test fails. |
46 |
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o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
47 |
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o move call to cal_readparms up to make calendar parameters/variable available |
48 |
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to all packages |
49 |
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|
50 |
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checkpoint58v_post |
51 |
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o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
52 |
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useDynP_inEos_Zc tested. |
53 |
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o pkg/exf: changes to properly interpolate/mask/scale initial fields |
54 |
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o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
55 |
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and portions thereof. See read_cs.txt for description and examples. |
56 |
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o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
57 |
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add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
58 |
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following the great-circle arc between those 2 points. |
59 |
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o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
60 |
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(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
61 |
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o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
62 |
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- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
63 |
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- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
64 |
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- still needs work (not working with some options ; efficiency to improve) |
65 |
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and serious testing. |
66 |
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- use this scheme for temperature & salinity in 2 advection test exp.: |
67 |
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advect_xy & advect_xz, respectively. |
68 |
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|
69 |
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checkpoint58u_post |
70 |
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o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
71 |
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o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
72 |
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o testreport: add option "-skipdir" to skip some test. |
73 |
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o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
74 |
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momentum calculation. |
75 |
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o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
76 |
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o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
77 |
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remove checkpoint.F and the_correction_step.F (no longer used); |
78 |
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do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
79 |
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o add option (linFSConserveTr) to correct for tracer source/sink due to |
80 |
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Linear Free surface |
81 |
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o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
82 |
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o pkg/thsice: fix reading mnc-pickups |
83 |
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|
84 |
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checkpoint58t_post |
85 |
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o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
86 |
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o pkg/mdsio: |
87 |
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- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
88 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
89 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
90 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
91 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
92 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
93 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
94 |
|
informations (variable names, time ...) to meta files. |
95 |
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- modify rdmds.m to give back the meta file content. |
96 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
97 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
98 |
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add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
99 |
|
diagnostic pointer. |
100 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
101 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
102 |
|
o fix multi-category seaice: |
103 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
104 |
|
SEAICE_MULTICATEGORY |
105 |
|
- fix short wave heat flux |
106 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
107 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
108 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
109 |
|
o Initial check-in of lab_sea adjoint |
110 |
|
(very similar to natl_box_adjoint/code_seaice) |
111 |
|
* used C-grid and EVP solver |
112 |
|
* used KPP, GM/Redi |
113 |
|
* uses inAdExact=.TRUE. |
114 |
|
* gradient checks fail for both ADM and TLM |
115 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
116 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
117 |
|
issue is related to forward mismatch between g77 an ifort |
118 |
|
o pkg/seaice: overhaul of thermodynamics |
119 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
120 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
121 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
122 |
|
make them 2D (FICE/QNETO/ ...) |
123 |
|
- remove FO (it is the same as QNETO) |
124 |
|
- introduce a few local fields to avoid modifying external fields such |
125 |
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as atemp, etc. |
126 |
|
|
127 |
|
checkpoint58s_post |
128 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
129 |
|
changed exf_set_gen.F so that |
130 |
|
genperiod=0 means input file is one time-constant field and |
131 |
|
genperiod=-12 means input file contains 12 monthly means |
132 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
133 |
|
this affects truncation error ; generate new output file for exp. which |
134 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
135 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
136 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
137 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
138 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
139 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
140 |
|
o start implementation of deep-atmosphere and anelastic formulation |
141 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
142 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
143 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
144 |
|
o profiles: fix for multithreaded case |
145 |
|
|
146 |
|
o diagnostics: rename few diags: |
147 |
|
s/'PRESSURE'/'RCENTER '/g |
148 |
|
s/'TICE '/'oceFreez'/g |
149 |
|
s/'TAUX '/'oceTAUX '/g |
150 |
|
s/'TAUY '/'oceTAUY '/g |
151 |
|
s/'SWFLUX '/'oceQsw '/g |
152 |
|
s/DIFx/DFxE/g |
153 |
|
s/DIFy/DFyE/g |
154 |
|
and add few ocean-forcing diagnostics: |
155 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
156 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
157 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
158 |
|
as actual snow thickness. It now refers everywhere to effective snow |
159 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
160 |
|
|
161 |
|
checkpoint58r_post |
162 |
|
o modifications to pkg/seaice/growth.F, which change results of |
163 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
164 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
165 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
166 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
167 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
168 |
|
both are turned off by default and do no change any results |
169 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
170 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
171 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
172 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
173 |
|
in natl_box (affects results @ truncation level: update output.txt) |
174 |
|
o multi-threading and IO: |
175 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
176 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
177 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
178 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
179 |
|
affects the results (but none of the verification test uses this scheme). |
180 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
181 |
|
(will certainly be subject to changes) |
182 |
|
o ctrl: adding new control variables: |
183 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
184 |
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|
185 |
|
checkpoint58q_post |
186 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
187 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
188 |
|
high_res_cube configuration by 4% on Columbia. |
189 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
190 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
191 |
|
dynamical allocation (seems to work in multi-threaded). |
192 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
193 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
194 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
195 |
|
|
196 |
|
checkpoint58p_post |
197 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
198 |
|
o shelfice: |
199 |
|
- fix a sign error so that no slip at shelfice interface works |
200 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
201 |
|
not mean, that the results are correct, but at least they are numerically |
202 |
|
stable |
203 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
204 |
|
o added adjoint exch routined for all exch*3d* routines |
205 |
|
and updated flow directives |
206 |
|
|
207 |
|
checkpoint58o_post |
208 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
209 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
210 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
211 |
|
and clean-up reading/writing of pickup files. |
212 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
213 |
|
o simplify EXCH interface: |
214 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
215 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
216 |
|
o added the regrid package |
217 |
|
o shelfice: |
218 |
|
- add a simple boundary layer scheme to reduce noise |
219 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
220 |
|
|
221 |
|
checkpoint58n_post |
222 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
223 |
|
local variable (not in common block). |
224 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
225 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
226 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
227 |
|
to work with SingleCpuIO. |
228 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
229 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
230 |
|
o multi-threading and IO: |
231 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
232 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
233 |
|
- barrier before and after reading. |
234 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
235 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
236 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
237 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
238 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
239 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
240 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
241 |
|
|
242 |
|
checkpoint58m_post |
243 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
244 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
245 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
246 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
247 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
248 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
249 |
|
add MITgcm_tutorials (= code + all the tutorials) |
250 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
251 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
252 |
|
o profiles: adding ptracer and ssh |
253 |
|
o testreport: change multi-test output-file name |
254 |
|
(from output.txt.{name} to output.{name}.txt) |
255 |
|
o profiles: now ok for mutli-tiles case |
256 |
|
o seaice: add 4 parameters for different advection schemes for area, |
257 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
258 |
|
is the standard parameter SEAICEadvScheme |
259 |
|
o calc_gw: |
260 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
261 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
262 |
|
of tutorial_plume_on_slope. |
263 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
264 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
265 |
|
update rotating_tank results, but not plume_on_slope (affected at |
266 |
|
truncation level, 11 digits). |
267 |
|
|
268 |
|
checkpoint58l_post |
269 |
|
o calc_gw: |
270 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
271 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
272 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
273 |
|
o commit code to make SST/SSS weights spatially variable |
274 |
|
(based on either variable in-situ or variable initial T/S weights) |
275 |
|
o pkg/ecco: |
276 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
277 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
278 |
|
* cost_averagesflags now returns year indices in addition to day, month |
279 |
|
* sflux balance is performed on annual basis |
280 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
281 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
282 |
|
including separate counting and multipliers |
283 |
|
o pkg/rbcs |
284 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
285 |
|
|
286 |
|
checkpoint58k_post |
287 |
|
o testreport: |
288 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
289 |
|
& running in input) |
290 |
|
- run in dir run (if it exists), in build otherwise. |
291 |
|
- call prepare_run (if input/prepare_run exists) |
292 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
293 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
294 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
295 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
296 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
297 |
|
o pkg/exf/exf_check_range.F |
298 |
|
- add tile index to diagnostics and move stop statement to the very |
299 |
|
end of the routine. |
300 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
301 |
|
define title of isomorphic variables according to the current config. |
302 |
|
o pkg/thsice with pkg/seaice dynamics: |
303 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
304 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
305 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
306 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
307 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
308 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
309 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
310 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
311 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
312 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
313 |
|
o tracer advection: |
314 |
|
- clean-up and simplify calc_common_factors.F |
315 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
316 |
|
advection subroutine (but still not used within DST advection S/R) |
317 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
318 |
|
|
319 |
|
checkpoint58j_post |
320 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
321 |
|
from file (collects calls previously in FORWARD_STEP) |
322 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
323 |
|
o adjoint store dir. adjusted accordingly |
324 |
|
o genmake2 |
325 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
326 |
|
|
327 |
|
checkpoint58i_post |
328 |
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
329 |
on wind stress (SEAICEstressFactor defaults to 1.) |
on wind stress (SEAICEstressFactor defaults to 1.) |
330 |
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
o Total number of Timers is finite (<=40): comment out 2 non-essential one |