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 gad_som : fix flux output (& diagnostics) to have same units as other |
8 |
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advection scheme fluxes (was previously multiplied by deltaT). |
9 |
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o added verification/seaice_obcs both to test seaice open boundaries |
10 |
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and to provide an example matlab scrpt for generating them |
11 |
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o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
12 |
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o pkg/salt_plume: clean up salt_plume_frac.F to |
13 |
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remove redundancy in PlumeMethod 1 and 4 |
14 |
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o pkg/kpp: added saltplume diagnostics |
15 |
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o pkg/obcs and pkg/seaice: |
16 |
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- do not set uice and vice to zero when OB*icefile are unspecified |
17 |
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- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
18 |
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- moved seaice tracer obcs after call to seaice_growth |
19 |
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o pkg/salt_plume: added various options for salt plume depth |
20 |
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criterion and for vertical distribution of the salt |
21 |
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|
22 |
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checkpoint59l |
23 |
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o pkg/ptracers: new version of ptracers pickup: |
24 |
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read meta file and write only fields which are needed to restart. |
25 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
26 |
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o pkg/seaice: |
27 |
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- add timescale for melting due to warm mixed layer as a means of |
28 |
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setting SEAICE_availHeatFrac more conveniently |
29 |
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- add a CPP-flag/runtime parameter check for flooding algorithm |
30 |
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- reformulated availHeat in seaice_growth.F to be independent of AREA |
31 |
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o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
32 |
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unit changes |
33 |
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o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
34 |
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o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
35 |
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SX vector computer. |
36 |
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o pkg/seaice: |
37 |
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- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
38 |
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seaice forcing fields can now be read only through pkg/exf |
39 |
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- removed some unused halos |
40 |
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o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
41 |
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o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
42 |
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or U/VICE from U/VWIND before computing U/VSTRESS |
43 |
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|
44 |
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checkpoint59k |
45 |
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o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
46 |
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dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
47 |
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o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
48 |
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all experiments pass when compile with un-initialised var. checking option. |
49 |
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o added pkg/salt_plume |
50 |
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o script to test restart (for now, in MITgcm_contrib/jmc_script) |
51 |
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o pkg/seaice: new read/write pickup version. |
52 |
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read meta file and write only fields which are needed to restart. |
53 |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
54 |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
55 |
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o lab_sea.hb87: modify the domain & update output.hb87.txt : |
56 |
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lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
57 |
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at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
58 |
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process. Fixed here by closing the domain at the Northern boundary. |
59 |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
60 |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
61 |
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a set of consecutive levels in/from a 3-D array. |
62 |
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o pkg/ptracers: |
63 |
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use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
64 |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
65 |
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|
66 |
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checkpoint59j |
67 |
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o in pkgs: dic, obcs, offline, rbcs: |
68 |
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standard way to compute coeff. for time interpolation between 2 time reccords |
69 |
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which retains full precision (& make results less dependent on compiler). |
70 |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
71 |
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o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
72 |
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packages instead of reading ice cover and wind speed separately |
73 |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
74 |
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(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
75 |
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to allow to compile customized code before the update) |
76 |
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o cleaning-up: |
77 |
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- fix CPP instruction syntax in pkg/obcs |
78 |
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- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
79 |
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add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
80 |
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- fix some threads issue in IO parts. |
81 |
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o pkg/dic: |
82 |
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- add tons of "_d 0" (--> much better testreports !) |
83 |
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and then update outputs of tutorial_global_oce_biogeo |
84 |
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o pkg/mom_fluxform: |
85 |
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add a special version of momentum advection intended to conserve momentum |
86 |
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next to a bathymetry step or a coastline edge. (default = off = #undef) |
87 |
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o new read/write pickup version: |
88 |
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- for now, only implemented for main (mdsio) pickup file. |
89 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
90 |
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and main pickup together. |
91 |
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- read meta file; read only what is needed to restart; stop if a field |
92 |
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is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
93 |
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if it make sense (even if the restart is not perfect). |
94 |
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- if no meta file, assume that pickup to read corresponds exactly to |
95 |
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a pickup that would currently be written. |
96 |
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- read pickup written in the old format (until checkpoint59i) if it |
97 |
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recognizes an old meta file (no field-list). |
98 |
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- add a meta file in exp. which starts from a pickup: 2 cases: |
99 |
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a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
100 |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
101 |
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b) a meta file describing the content of the associated pickup file |
102 |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
103 |
|
o pkg/mdsio & pkg/rw: |
104 |
|
- new routine to read a meta file ; new set of routine to read |
105 |
|
Multiple-fields file (with meta file). |
106 |
|
o added open boundary conditions capability for seaice |
107 |
|
HSNOW, HSALT, UICE, and VICE |
108 |
|
|
109 |
|
checkpoint59i |
110 |
|
o adjoint: |
111 |
|
* fix multiDimAdvection adjoint |
112 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
113 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
114 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
115 |
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NLFS and multiDimAdvection using DST3 (=30) |
116 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
117 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
118 |
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update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
119 |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
120 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
121 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
122 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
123 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
124 |
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as argument. (only atm2d & obcs write_pickup have not yet been updated) |
125 |
|
o pkg/monitor: |
126 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
127 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
128 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
129 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
130 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
131 |
|
thermodynamics |
132 |
|
- requires a little reorganization, which affects the testreport results |
133 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
134 |
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so that now the conservative form is tested |
135 |
|
- add a few comments |
136 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
137 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
138 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
139 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
140 |
|
thermodynamic growth rates |
141 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
142 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
143 |
|
Affects results @ truncation level (cg2d match) and update output of |
144 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
145 |
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global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
146 |
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+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
147 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
148 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
149 |
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|
150 |
|
checkpoint59h |
151 |
|
o pkg/exf: |
152 |
|
- improve vectorization by moving if-statement out of loops in |
153 |
|
exf_mapfields, exf_radiation |
154 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
155 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
156 |
|
o testreport: |
157 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
158 |
|
monitor & update offline_exf_seaice exp. output. |
159 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
160 |
|
o pkg/seaice: |
161 |
|
- bug fix in the evp solver: boundary conditions were affected be |
162 |
|
masking of zMax/zMin (changes results) |
163 |
|
- minor bug fix in boundary conditions in seaice_calc_strainrates |
164 |
|
(changes results for no_slip) |
165 |
|
- seaice_lsr.F: make interpolation of eta dependent on boundaries |
166 |
|
- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
167 |
|
- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
168 |
|
stress formulation and no-slip boundary conditions |
169 |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
170 |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
171 |
|
o pkg/seaice: a first HSALT time stepping equation has been checked in |
172 |
|
o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
173 |
|
in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
174 |
|
without requiring DO-IF statements |
175 |
|
o pkg/thsice: |
176 |
|
use continuous power-law function for partition of energy between lateral |
177 |
|
melting/freezing and thinning/thickening ; old code using step function |
178 |
|
still available with #undef THSICE_FRACEN_POWERLAW |
179 |
|
update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
180 |
|
o testreport: change AD testing : check against results/output_adm.txt |
181 |
|
using same scripts as for forward test. |
182 |
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|
183 |
|
checkpoint59g |
184 |
|
o adjoint testing: in preparation for changing testreport: |
185 |
|
- output format: cost and grad written on separated lines |
186 |
|
- ad output results in directory "results" (instead of "results_ad") |
187 |
|
o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
188 |
|
o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
189 |
|
o pkg/ecco: allow user defined cost function contributions |
190 |
|
o testreport: |
191 |
|
Allow to choose (per experiment) the list of tested output variables |
192 |
|
and the main variable (used to issue a pass/FAIL ) ; |
193 |
|
- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
194 |
|
- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
195 |
|
Also modify printing of summary: |
196 |
|
a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
197 |
|
b) echo the list of tested variables in the individual summary.txt of |
198 |
|
each experiment. |
199 |
|
o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
200 |
|
threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
201 |
|
(but still depend on the tile decompostion of the domain). |
202 |
|
o pkg/seaice: change a discretization detail to make the B-grid code |
203 |
|
"more symmetric". This change is likely to remove all "ridges/leads" that |
204 |
|
where quasi-aligned with the grid in B-grid solutions. It may also be |
205 |
|
the solution to the stress coupling issues with the B-grid. |
206 |
|
o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
207 |
|
remove .cvsignore from input dir. (since testreport no longer run here). |
208 |
|
o pkg/thsice: |
209 |
|
- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
210 |
|
- fix reshaping of sea-ice just after advection: |
211 |
|
melt all the ice only if ice-volume is too small. |
212 |
|
- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
213 |
|
prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
214 |
|
and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
215 |
|
o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
216 |
|
tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
217 |
|
o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
218 |
|
forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
219 |
|
(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
220 |
|
and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
221 |
|
of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
222 |
|
-> update output.txt |
223 |
|
o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
224 |
|
this affects truncation error: -> update output.txt of exp: |
225 |
|
global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
226 |
|
ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
227 |
|
|
228 |
|
checkpoint59f |
229 |
|
o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
230 |
|
o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
231 |
|
a bounded range (in forward mode) |
232 |
|
o pkg/ecco, ctrl, autodiff and mom_common: |
233 |
|
internal parameter controls, completements of implementations |
234 |
|
o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
235 |
|
o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
236 |
|
(not seem any difference in testing results). |
237 |
|
o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
238 |
|
at face corners. |
239 |
|
o pkg/generic_advdiff: |
240 |
|
- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
241 |
|
loop range indices for computing vertical advection tendency |
242 |
|
and do the calculation in the interior only (no overlap) ; |
243 |
|
for now, only implemented for SOM advection (to save CPU time). |
244 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
245 |
|
o exch2 adjoint |
246 |
|
First set of changes: |
247 |
|
- add exch2 hand-written adjoint templates |
248 |
|
- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
249 |
|
This will require cleanup in pkg/autodiff/*.F |
250 |
|
(changed routines currently kept separate in verif. code/) |
251 |
|
- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
252 |
|
that used to hide exch2 or cubed-sphere specific code |
253 |
|
(commented via 'cph-exch2') |
254 |
|
o pkg/seaice |
255 |
|
- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
256 |
|
o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
257 |
|
output of global_ocean.cs32x15.thsice . |
258 |
|
|
259 |
|
checkpoint59e |
260 |
|
o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
261 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
262 |
|
when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
263 |
|
o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
264 |
|
(#ifdef ALLOW_SALT_PLUME) |
265 |
|
o gather_2d/scatter_2d: removed halo regions |
266 |
|
o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
267 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
268 |
|
only available with Skew-flux form and not yet tested in realistic set-up. |
269 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
270 |
|
so maybe GM/Redi adjoint is now broken. |
271 |
|
o seaice adjoint |
272 |
|
* add AREA, HEFF, HSNOW as control variable |
273 |
|
(should not change lab_sea results) |
274 |
|
* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
275 |
|
o pkg/seaice: |
276 |
|
* added computation of saltFlux in seaice_growth; |
277 |
|
For time being, sea ice salinity is assumed constant |
278 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
279 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
280 |
|
defaults to 0.0 in order to maintain backward compatibility. |
281 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
282 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
283 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
284 |
|
heat content used to melt or grow ice |
285 |
|
* commented out cap of HICE: it helps keep ice thinner |
286 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
287 |
|
* applied OBCS T/S mask to HEFFM sea ice mask |
288 |
|
|
289 |
|
checkpoint59d |
290 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
291 |
|
for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
292 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
293 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
294 |
|
and change default value of parameter "GM_Small_Number"; |
295 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
296 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
297 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
298 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
299 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
300 |
|
o pkg/seaice: |
301 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
302 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
303 |
|
changes verification/lab_sea |
304 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
305 |
|
read, understand, and debug. This causes changes at the truncation level. |
306 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
307 |
|
part) of the LSR solver. Changes all LSR results. |
308 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
309 |
|
is initilized with small values - does not change lab_sea results. |
310 |
|
- added HsnowFile initialization capability |
311 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
312 |
|
initialization of pkg/smooth and application to control vector |
313 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
314 |
|
o dependencies: pkg/profiles requires pkg/cal |
315 |
|
o pkg/profiles: |
316 |
|
- added option ALLOW_PROFILES_GENERICGRID |
317 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
318 |
|
that interpolation information (grid points and coefficients) is provided |
319 |
|
within the netcdf input files. |
320 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
321 |
|
that allow you to prepare netcdf input files. |
322 |
|
- also modified: cleaner include statements, cleaner error print statements, |
323 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
324 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
325 |
|
o pkg/seaice: |
326 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
327 |
|
requires a new routine: seaice_diagnostics_fill.F |
328 |
|
- make sure that seaice does not move if not forced (pressure replacement |
329 |
|
method, Hibler and Ip, 1995), changes results |
330 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
331 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
332 |
|
It is turned off by default (=-1.), because it changes the results. |
333 |
|
- make it possible to read AREA from a file, too. |
334 |
|
|
335 |
|
checkpoint59c |
336 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
337 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
338 |
|
o pkg/thsice: |
339 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
340 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
341 |
|
o pkg/obcs: |
342 |
|
- bug fix for balance code |
343 |
|
o pkg/seaice: |
344 |
|
- allow values of SEAICE_elasticParm > 1 |
345 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
346 |
|
to SEAICE_elasticParm |
347 |
|
- make lsr boundary conditions free slip (by default), changes result |
348 |
|
- add code for no slip boundary conditions for lsr |
349 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
350 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
351 |
|
o change calculation of Visbeck K: |
352 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
353 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
354 |
|
clipping or linear tappering. |
355 |
|
- fix vertical averaging (wrong by 1/2 level) |
356 |
|
- leave the old version (but will not be maintained) within |
357 |
|
#ifdef OLD_VISBECK_CALC / #endif |
358 |
|
- update output of exp. ideal_2D_oce |
359 |
|
o change error catch in calc_r_star to improve vectorization |
360 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
361 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
362 |
|
o adjoint: |
363 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
364 |
|
(but with modifs/completions/cleanups) |
365 |
|
Storing is now bundled into large arrays to optimized I/O |
366 |
|
(and second step in cleanup of the_main_loop) |
367 |
|
|
368 |
|
checkpoint59b |
369 |
|
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
370 |
|
- export/import (between ocean & coupler) fields needed for ocean DIC. |
371 |
|
o pkg/seaice: |
372 |
|
- get rid of three more exchanges seaice_calc_viscosities (required |
373 |
|
different loop boundaries in seaice_lsr and seaice_ocean_stress) |
374 |
|
- bug fix in seaice_ocean_stress (update of lab_sea required) |
375 |
|
- reduce loop boundaries to necessary minimum also in seaice_evp |
376 |
|
- go back to the old way of computing deltaC/Z as the adjoint likes that |
377 |
|
better |
378 |
|
o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
379 |
|
passive tracer to an Age Tracer) + update output.txt |
380 |
|
o pkg/exf: |
381 |
|
- implement A-grid / C-grid selection for wind-stress input files. |
382 |
|
- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
383 |
|
for now, in exf_bulk_largeyeager04.F only : |
384 |
|
- change implementation for case where windspeed + 2. components wind-stress |
385 |
|
are read-in. AND use rhoConstFresh to convert evap. |
386 |
|
o pkg/seaice: |
387 |
|
- use correct EXCH_UV for wind-forcing (on A-grid). |
388 |
|
- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
389 |
|
SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
390 |
|
o pkg/exf: |
391 |
|
- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
392 |
|
EXF_INTERPOLATION: |
393 |
|
- merge global_with_exf/code version of exf_interp_read.F |
394 |
|
to the main code ; |
395 |
|
- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
396 |
|
reading the file ; Important: This options needs to be defined to recover |
397 |
|
previous code. |
398 |
|
otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
399 |
|
- no longer loose real*8 precision along the way when using exf_iprec=64. |
400 |
|
o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
401 |
|
- change discretisation of evp-solver in order to avoid another exchange |
402 |
|
(changes lab_sea) and clean up a little |
403 |
|
- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
404 |
|
help the adjoint (this also changes the results slightly) |
405 |
|
- add a few "_d 0" where they had been missing in seaice_evp.F |
406 |
|
- cleaning up: remove unused seaice_calc_rhs.F |
407 |
|
o pkg/exf: some cleaning-up: |
408 |
|
- change various "constants" into runtime parameters |
409 |
|
- cleaned-up Large&Yeager04 routine which should eventually |
410 |
|
replace exf_bulkformulae.F (changed names of S/R and CPP) |
411 |
|
and merged various ALLOW_ATM_WIND options |
412 |
|
only used with thsice pkg (in thsice_get_exf.F): |
413 |
|
- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
414 |
|
which are used when useStabilityFct_overIce=TRUE (= the default) |
415 |
|
- change default values of ice & snow emissivity and scale downward LW |
416 |
|
by ice & snow emissivity. |
417 |
|
o pkg/thsice: |
418 |
|
fix few little problems, in thsice_calc_thickn.F: |
419 |
|
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
420 |
|
- melt only laterally if hIce < hThinIce (as the comments say) |
421 |
|
and in thsice_extend.F: |
422 |
|
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
423 |
|
- start to form ice as soon as the minimum ice-volume is reachable. |
424 |
|
update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
425 |
|
and cpl_aim+ocn |
426 |
|
o pkg/kpp |
427 |
|
- move computation of surface related input fields to KPP into a new |
428 |
|
subroutine kpp_forcing_surf.F |
429 |
|
- remove wrong (within bi,bj loops) EXCH calls. |
430 |
|
- little cleaning (add argument myThid in last position, cvs header ...) |
431 |
|
- for now, fix conservation problem by exchanging KPPviscAz (may not |
432 |
|
be the best fix) |
433 |
|
o pkg/seaice |
434 |
|
- check for inconsistent evp parameter/cpp-flag combination |
435 |
|
- remove leftover errIO flat for obsolete name list error handling |
436 |
|
o OpenAD |
437 |
|
- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
438 |
|
|
439 |
|
checkpoint59a |
440 |
|
o pkg/seaice: some parameter clarifications and a little bit of clean up |
441 |
|
o pkg/thsice: rename run-time parameters: |
442 |
|
himin -> hIceMin |
443 |
|
himin0 -> hThinIce |
444 |
|
hihig -> hThickIce |
445 |
|
i0 -> i0swFrac |
446 |
|
transCoef -> bMeltCoef |
447 |
|
frac_energy -> fracMelting |
448 |
|
add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
449 |
|
with default values (for now) that do not change the results. |
450 |
|
remove old version of thsice vars advection in pkg/seaice. |
451 |
|
o in FFIELDS.h: |
452 |
|
- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
453 |
|
- make pLoad & sIceLoad always available (but still only used if |
454 |
|
ATMOSPHERIC_LOADING is #define). |
455 |
|
o pkg/kpp: replaced _KPP_RL with _RL |
456 |
|
o bug fixes for vertical diffusivity computations when both KPP and |
457 |
|
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
458 |
|
are no longer updating the vertical diffusivity array |
459 |
|
(passed as argument) but are (re-) setting those arrays. |
460 |
|
o pkg/seaice: fix bug in evp solver, while doing that |
461 |
|
- change (improve?) discretization of stress computations for both |
462 |
|
cgrid-lsr and evp solver |
463 |
|
- add a new routine to compute strain rates |
464 |
|
- the above changes lab_sea results |
465 |
|
- add no slip conditions for evp solver (off by default), lsr-version |
466 |
|
may follow |
467 |
|
- fix exchange for shear at Z-points (does not change lab_sea) |
468 |
|
- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
469 |
|
(to force the user to pick a time step since there is not "safe" way |
470 |
|
of choosing it) |
471 |
|
- add principal stress diagnostics |
472 |
|
- rearrange fields for evp a little to avoid having to call a: too many |
473 |
|
exchanges and b: exchanges for stress trensor components which we do |
474 |
|
not have. |
475 |
|
- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
476 |
|
of evp, complete rewrite for lsr case (latter is does not yet work |
477 |
|
in all cases) |
478 |
|
o pkg/kpp: add code to have mixing in shelf ice caverns |
479 |
|
- add myThid to all kpp routines (long overdue) |
480 |
|
|
481 |
|
checkpoint59 |
482 |
|
o pkg/exf: |
483 |
|
- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
484 |
|
ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
485 |
|
- move exf header files from lower_case.h to UPPER_CASE.h ; |
486 |
|
add missing cvs Header & Name |
487 |
|
- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
488 |
|
- add namelist param. selectStressGridPosition, exf_monFreq |
489 |
|
- retire many _CLIM routines, and remove data.exf_clim |
490 |
|
+ params moved to data.exf |
491 |
|
+ climsst, climsss now handled by exf_set_gen, i.e. |
492 |
|
climss?period=0 refers to constant field, |
493 |
|
climss?period=-12 to monthly forcing |
494 |
|
- split up namelists in data.exf |
495 |
|
o pkg/seaice: |
496 |
|
- remove seaice_exch and seaice_exch_uv |
497 |
|
- remove superfluous exchange of theta |
498 |
|
- add myThid to seaice_budget_ocean/ice |
499 |
|
- add new interface for atmospheric wind forcing (C-grid only) |
500 |
|
+ new routine |
501 |
|
+ two new field (taux, tauy for stress over ice) |
502 |
|
+ removed one global field (DAIRN) for C-grid case only |
503 |
|
o pkg/thsise |
504 |
|
- 2nd set of modifs for thsice adjoint in conjunction with exf |
505 |
|
o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
506 |
|
|
507 |
|
checkpoint58y_post |
508 |
|
o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
509 |
|
vertical diffusivity, similar to that in MOM4; turned on using |
510 |
|
#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
511 |
|
diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
512 |
|
o Added capability for 3D specification of background vertical diffusion |
513 |
|
coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
514 |
|
in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
515 |
|
"data" file that contains the 3D vertical diffusivity coefficients. |
516 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
517 |
|
- add code within pkg thsice to advect & diffuse sea-ice fields |
518 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
519 |
|
but: - conserving Mass, Heat & Salt. |
520 |
|
- better when using non-linear advection scheme (not yet fully tested) |
521 |
|
- can also be used in atmospheric set-up (for now, only the diffusion). |
522 |
|
|
523 |
|
checkpoint58x_post |
524 |
|
o IO option for global-file compact format: |
525 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
526 |
|
- add I/O capability (pkg/mdsio). |
527 |
|
- adapt utils/matlab/rdmds.m to read this format. |
528 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
529 |
|
o shelfice: add a few diagnostics |
530 |
|
|
531 |
|
checkpoint58w_post |
532 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
533 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
534 |
|
(and replace horiVertRatio in NH code). |
535 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
536 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
537 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
538 |
|
directly to drive seaice model (C-grid only) |
539 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
540 |
|
- reintroduce computation of wind from stress, |
541 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
542 |
|
mass points to avoid tau = 0 |
543 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
544 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
545 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
546 |
|
(tested on all testreport mnc output files). |
547 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
548 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
549 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
550 |
|
to all packages |
551 |
|
|
552 |
|
checkpoint58v_post |
553 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
554 |
|
useDynP_inEos_Zc tested. |
555 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
556 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
557 |
|
and portions thereof. See read_cs.txt for description and examples. |
558 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
559 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
560 |
|
following the great-circle arc between those 2 points. |
561 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
562 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
563 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
564 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
565 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
566 |
|
- still needs work (not working with some options ; efficiency to improve) |
567 |
|
and serious testing. |
568 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
569 |
|
advect_xy & advect_xz, respectively. |
570 |
|
|
571 |
|
checkpoint58u_post |
572 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
573 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
574 |
|
o testreport: add option "-skipdir" to skip some test. |
575 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
576 |
|
momentum calculation. |
577 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
578 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
579 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
580 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
581 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
582 |
|
Linear Free surface |
583 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
584 |
|
o pkg/thsice: fix reading mnc-pickups |
585 |
|
|
586 |
|
checkpoint58t_post |
587 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
588 |
|
o pkg/mdsio: |
589 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
590 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
591 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
592 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
593 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
594 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
595 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
596 |
|
informations (variable names, time ...) to meta files. |
597 |
|
- modify rdmds.m to give back the meta file content. |
598 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
599 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
600 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
601 |
|
diagnostic pointer. |
602 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
603 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
604 |
|
o fix multi-category seaice: |
605 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
606 |
|
SEAICE_MULTICATEGORY |
607 |
|
- fix short wave heat flux |
608 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
609 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
610 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
611 |
|
o Initial check-in of lab_sea adjoint |
612 |
|
(very similar to natl_box_adjoint/code_seaice) |
613 |
|
* used C-grid and EVP solver |
614 |
|
* used KPP, GM/Redi |
615 |
|
* uses inAdExact=.TRUE. |
616 |
|
* gradient checks fail for both ADM and TLM |
617 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
618 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
619 |
|
issue is related to forward mismatch between g77 an ifort |
620 |
|
o pkg/seaice: overhaul of thermodynamics |
621 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
622 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
623 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
624 |
|
make them 2D (FICE/QNETO/ ...) |
625 |
|
- remove FO (it is the same as QNETO) |
626 |
|
- introduce a few local fields to avoid modifying external fields such |
627 |
|
as atemp, etc. |
628 |
|
|
629 |
|
checkpoint58s_post |
630 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
631 |
|
changed exf_set_gen.F so that |
632 |
|
genperiod=0 means input file is one time-constant field and |
633 |
|
genperiod=-12 means input file contains 12 monthly means |
634 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
635 |
|
this affects truncation error ; generate new output file for exp. which |
636 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
637 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
638 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
639 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
640 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
641 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
642 |
|
o start implementation of deep-atmosphere and anelastic formulation |
643 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
644 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
645 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
646 |
|
o profiles: fix for multithreaded case |
647 |
|
|
648 |
|
o diagnostics: rename few diags: |
649 |
|
s/'PRESSURE'/'RCENTER '/g |
650 |
|
s/'TICE '/'oceFreez'/g |
651 |
|
s/'TAUX '/'oceTAUX '/g |
652 |
|
s/'TAUY '/'oceTAUY '/g |
653 |
|
s/'SWFLUX '/'oceQsw '/g |
654 |
|
s/DIFx/DFxE/g |
655 |
|
s/DIFy/DFyE/g |
656 |
|
and add few ocean-forcing diagnostics: |
657 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
658 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
659 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
660 |
|
as actual snow thickness. It now refers everywhere to effective snow |
661 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
662 |
|
|
663 |
|
checkpoint58r_post |
664 |
|
o modifications to pkg/seaice/growth.F, which change results of |
665 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
666 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
667 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
668 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
669 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
670 |
|
both are turned off by default and do no change any results |
671 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
672 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
673 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
674 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
675 |
|
in natl_box (affects results @ truncation level: update output.txt) |
676 |
|
o multi-threading and IO: |
677 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
678 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
679 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
680 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
681 |
|
affects the results (but none of the verification test uses this scheme). |
682 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
683 |
|
(will certainly be subject to changes) |
684 |
|
o ctrl: adding new control variables: |
685 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
686 |
|
|
687 |
|
checkpoint58q_post |
688 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
689 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
690 |
|
high_res_cube configuration by 4% on Columbia. |
691 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
692 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
693 |
|
dynamical allocation (seems to work in multi-threaded). |
694 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
695 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
696 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
697 |
|
|
698 |
checkpoint58p_post |
checkpoint58p_post |
699 |
o obcs: stop if obcs is used with useCDscheme = .true. |
o obcs: stop if obcs is used with useCDscheme = .true. |
700 |
o shelfice: |
o shelfice: |