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 fix a bug in diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
8 |
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o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
9 |
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and rename: |
10 |
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ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
11 |
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ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
12 |
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o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
13 |
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|
14 |
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checkpoint61c |
15 |
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o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
16 |
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to add mass source/sink of fluid in the interior (3-D generalisation |
17 |
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of oceanic real-fresh water flux). |
18 |
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o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
19 |
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o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
20 |
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o new pkg: down_slope |
21 |
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density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
22 |
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- presently, modify T & S inland (dwnslp_calc_rho.F). |
23 |
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can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
24 |
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- implementation for ocean in P-coords not tested. |
25 |
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- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
26 |
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o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
27 |
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(to facilitate conversion of oceanic pkg to p-coordinate). |
28 |
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o change FIND_RHO to FIND_RHO_2D : |
29 |
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pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
30 |
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o new pkg: cheapaml |
31 |
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|
32 |
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checkpoint61b |
33 |
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o exch2: |
34 |
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change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
35 |
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- no longer depend on the order sequence (N,S,E,W). |
36 |
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- 3rd exchange no longer needed (tested with 24 tiles). |
37 |
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- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
38 |
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- exch_UV_A-grid readily available (but not yet tested). |
39 |
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comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
40 |
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(both are no longer needed) in exch_uv: no effect in forward run; but |
41 |
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get truncation error differences with adjoint exch. |
42 |
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o exch2: |
43 |
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- change index-bounds storage (moved from target to local tile, |
44 |
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more intuitive this way) ; rename/remove some variables. |
45 |
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- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
46 |
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|
47 |
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checkpoint61a |
48 |
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o exch2/matlab-topology-generator: |
49 |
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fix bug in index bounds for N-S internal exchange (hard to tell if this |
50 |
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had any effect on the solution). |
51 |
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o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
52 |
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is exceeded |
53 |
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o testreport: modify syntax of awk, so that it works also with |
54 |
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awk, and not only with nawk and gawk |
55 |
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|
56 |
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checkpoint61 |
57 |
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o autodiff |
58 |
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Change default for TAF usage by removing argument '-nonew_arg' |
59 |
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This changes TAF subroutine argument list (ordering of active var.) |
60 |
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Omission of this flag leads to incompatibility w.r.t. TAMC |
61 |
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To restore TAMC-compatibility, need following modifs: |
62 |
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* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
63 |
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* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
64 |
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Tested TAF version is 1.9.22 |
65 |
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N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
66 |
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|
67 |
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checkpoint60 |
68 |
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--->>> This is the last checkpoint for which generating the adjoint |
69 |
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--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
70 |
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--->>> by default. |
71 |
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--->>> Future checkpoints will ommit this flag by default. |
72 |
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o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
73 |
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o pkg/grdchk: Add gradient check to etan0 perturbations. |
74 |
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o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
75 |
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o pkg/autodiff: more flexibility in zeroadj. |
76 |
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model/src: modifying do_oceanic_phys.F accordingly. |
77 |
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o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
78 |
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o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
79 |
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special setup of gmredi for which the adjoint is stable |
80 |
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enough for parameter optimization. |
81 |
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o bridging the gap between eddy stress and GM. |
82 |
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-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
83 |
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along with a change in CPP option (now ALLOW_EDDYPSI). |
84 |
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-> when using GM w/ GM_AdvForm: |
85 |
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The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
86 |
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is applied either in the tracer Eq. or in momentum Eq. |
87 |
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depending on data.gmredi (intro. GM_InMomAsStress). |
88 |
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-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
89 |
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The key modifications are in model/src/taueddy_external_forcing.F |
90 |
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pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
91 |
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|
92 |
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checkpoint59r |
93 |
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o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
94 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
95 |
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fix option to read coriolis(@ cell-corner) from files with CS-grid. |
96 |
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o pkg/mnc: add some attributes to standard 1D-coordinate variables |
97 |
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o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
98 |
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mass points, when using mnc for output |
99 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
100 |
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default (which is the value of getcon('UNDEF')) |
101 |
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o pkg/mnc: prepare mnc for the actual use of missing values with the |
102 |
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diagnostics package: small fix in mnc_cw_readwrite.template and more |
103 |
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initialisation of never used fields |
104 |
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- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
105 |
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versions |
106 |
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o pkg/thsice/thsice_ini_vars.F added default initial values so that |
107 |
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thermodynamics sea ice solver does not blow up when some initial fields |
108 |
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are missing. |
109 |
|
o move from external_forcing_surf.F to ini_forcing.F |
110 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
111 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
112 |
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o Freshen up a bit hs94.1x64x5, notably: |
113 |
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remove rotationPeriod and tRef=5*0. (adjoint only), and add |
114 |
|
exactConserv=.TRUE. |
115 |
|
o pkg/generic_advdiff: |
116 |
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change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
117 |
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applies to files where Temperature & Salinity 2nd Order moments are used. |
118 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
119 |
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this uses a dynamically allocated internal state data structure |
120 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
121 |
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and requires a fortran 90 compiler |
122 |
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|
123 |
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checkpoint59q |
124 |
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o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
125 |
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(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
126 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
127 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
128 |
|
- change EOS (POLY3 --> JMD95Z) |
129 |
|
- use Bryan-Lewis vertical diffusivity |
130 |
|
- use multidimensional advection |
131 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
132 |
|
- change a couple of parameters in dic pkg |
133 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
134 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
135 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
136 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
137 |
|
o implementation of TAF directives for gchem,cfc,dic |
138 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
139 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
140 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
141 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
142 |
|
--> changes results in exp4, seaice_obcs |
143 |
|
o tutorial_deep_convection : |
144 |
|
update the set-up and increase resolution and domain size ; start |
145 |
|
from pseudo initial conditions = output at t=120mn in order to see |
146 |
|
something happening when running testreport. |
147 |
|
o pkg/seaice: add os7mp as an advection scheme |
148 |
|
add check for advection schemes |
149 |
|
add a flag for restoring T and S underneath sea ice |
150 |
|
o pkg/my82: add netcdf-support and diagnostics |
151 |
|
o thsice pkg: |
152 |
|
- Now hsMax limits snow height by turning it into ice following |
153 |
|
flooding scheme (and now conserving energy) |
154 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
155 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
156 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
157 |
|
|
158 |
|
checkpoint59p |
159 |
|
o gchem / dic / cfc : |
160 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
161 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
162 |
|
- various re-arrangement in initialisation & header file ; |
163 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
164 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
165 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
166 |
|
before) providing pickupStrictlyMatch is set to False. |
167 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
168 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
169 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
170 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
171 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
172 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
173 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
174 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
175 |
|
scheme to use for vorticty-term ; |
176 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
177 |
|
(with default selectVortScheme, return to original discretisation) |
178 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
179 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
180 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
181 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
182 |
|
also fix diagnostics VISCAHW & VISCA4W. |
183 |
|
|
184 |
|
checkpoint59o |
185 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
186 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
187 |
|
move a few statemens out the main loop into separate loops |
188 |
|
o pkg/shelfice: |
189 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
190 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
191 |
|
rhoConstFresh=rhoConst (by accident) |
192 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
193 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
194 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
195 |
|
- convert potential temperature into in-situ temperature. This changes the |
196 |
|
isomip tests => update tests |
197 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
198 |
|
writing a pickup at the last timestep |
199 |
|
o tools/mpack-1.6 : |
200 |
|
- disable automake (not working) and autoconf (not needed). |
201 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
202 |
|
also cleaner with much less compilation warnings. |
203 |
|
o pkg/profiles: |
204 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
205 |
|
(for "less than 32 characters name" compiler requirement) |
206 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
207 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
208 |
|
o pkg/diagnostics (stats-diags): |
209 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
210 |
|
o genmake2: replace (4 times) |
211 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
212 |
|
with |
213 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
214 |
|
echo $COMM >> genmake_warnings |
215 |
|
$COMM >> genmake_warnings 2>&1 |
216 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
217 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
218 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
219 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
220 |
|
o pkg/ctrl: |
221 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
222 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
223 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
224 |
|
|
225 |
|
checkpoint59n |
226 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
227 |
|
number in dedicate array "hdiag": |
228 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
229 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
230 |
|
- many small changes (integer format) for large number of diagnostics |
231 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
232 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
233 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
234 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
235 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
236 |
|
geographical coordinates according to the inverse of the rotation defined |
237 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
238 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
239 |
|
Naturally, this feature does not work with all packages, so some |
240 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
241 |
|
profiles), because there the coordinates are assumed to be regular |
242 |
|
spherical grid coordinates. |
243 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
244 |
|
- introduce isopycnal diffusion coefficient control. |
245 |
|
o tools/adjoint_options: |
246 |
|
- additional control vector components. |
247 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
248 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
249 |
|
o pkg/mypackage: |
250 |
|
- add example of read/write pickup for state-var ; |
251 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
252 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
253 |
|
transitions for useExfYearlyFields |
254 |
|
- add new subroutine that determines the file to read from for |
255 |
|
use*YearlyFields = .TRUE. and .FALSE. |
256 |
|
- add a verification experiment to global_with_exf that tests |
257 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
258 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
259 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
260 |
|
subroutines (which could be generated from a template, because they are |
261 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
262 |
|
simplicity |
263 |
|
o pkg/exf: |
264 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
265 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
266 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
267 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
268 |
|
directive in routine lagran, and splitting a loop and making do while the |
269 |
|
outermost loop (the latter requires the intoduction of index arrays) |
270 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
271 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
272 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
273 |
|
o verification/seaice_obcs: updated for restart test and latest options |
274 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
275 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
276 |
|
for now this is only available for the C-grid code and also within |
277 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
278 |
|
|
279 |
|
checkpoint59m |
280 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
281 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
282 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
283 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
284 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
285 |
|
and to provide an example matlab scrpt for generating them |
286 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
287 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
288 |
|
remove redundancy in PlumeMethod 1 and 4 |
289 |
|
o pkg/kpp: added saltplume diagnostics |
290 |
|
o pkg/obcs and pkg/seaice: |
291 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
292 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
293 |
|
- moved seaice tracer obcs after call to seaice_growth |
294 |
|
o pkg/salt_plume: added various options for salt plume depth |
295 |
|
criterion and for vertical distribution of the salt |
296 |
|
|
297 |
|
checkpoint59l |
298 |
|
o pkg/ptracers: new version of ptracers pickup: |
299 |
|
read meta file and write only fields which are needed to restart. |
300 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
301 |
|
o pkg/seaice: |
302 |
|
- add timescale for melting due to warm mixed layer as a means of |
303 |
|
setting SEAICE_availHeatFrac more conveniently |
304 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
305 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
306 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
307 |
|
unit changes |
308 |
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
309 |
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
310 |
SX vector computer. |
SX vector computer. |
313 |
seaice forcing fields can now be read only through pkg/exf |
seaice forcing fields can now be read only through pkg/exf |
314 |
- removed some unused halos |
- removed some unused halos |
315 |
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
316 |
o pkg/exf: added CPP option EXF_SUBTRACT_UVVEL_FROM_UVWIND for subtracting |
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
317 |
UVEL and VVEL from UWIND and VWIND prior to applying bulk formulae. |
or U/VICE from U/VWIND before computing U/VSTRESS |
318 |
|
|
319 |
checkpoint59k |
checkpoint59k |
320 |
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
321 |
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
322 |
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
323 |
all experiments pass when compile with un-initilised var. checking option. |
all experiments pass when compile with un-initialised var. checking option. |
324 |
o added pkg/salt_plume |
o added pkg/salt_plume |
325 |
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
326 |
o pkg/seaice: new read/write pickup version. |
o pkg/seaice: new read/write pickup version. |