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 start implementation of deep-atmosphere and anelastic formulation |
8 |
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o verification: remove 2nd copy of input files and use script "prepare_run" |
9 |
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to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
10 |
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o mom_common/vecinv/fluxform: fix a few initialisation isssues |
11 |
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o profiles: fix for multithreaded case |
12 |
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|
13 |
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o diagnostics: rename few diags: |
14 |
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s/'PRESSURE'/'RCENTER '/g |
15 |
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s/'TICE '/'oceFreez'/g |
16 |
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s/'TAUX '/'oceTAUX '/g |
17 |
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s/'TAUY '/'oceTAUY '/g |
18 |
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s/'SWFLUX '/'oceQsw '/g |
19 |
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s/DIFx/DFxE/g |
20 |
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s/DIFy/DFyE/g |
21 |
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and add few ocean-forcing diagnostics: |
22 |
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atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
23 |
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o modifications to pkg/seaice/growth.F and budget.F, which change results of |
24 |
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lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
25 |
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as actual snow thickness. It now refers everywhere to effective snow |
26 |
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thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
27 |
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|
28 |
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checkpoint58r_post |
29 |
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o modifications to pkg/seaice/growth.F, which change results of |
30 |
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lab_sea experiment: fixes pertain to melting snow over open water, to |
31 |
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masking EVAP under sea ice, and to using the correct AREA variable for |
32 |
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computations of EVAP, PRECIP, HSNOW, and GHEFF |
33 |
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o add ability to read bathy, salt, and theta using MNC (off by def) |
34 |
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o add flooding algorithm and advection of HSNOW for pkg/seaice; |
35 |
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both are turned off by default and do no change any results |
36 |
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o seaice advection with pkg/thsice: a step toward the use of non-linear |
37 |
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advection scheme, but #ifdef or commented out for now (requires more EXCH). |
38 |
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o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
39 |
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(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
40 |
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in natl_box (affects results @ truncation level: update output.txt) |
41 |
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o multi-threading and IO: |
42 |
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- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
43 |
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- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
44 |
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(needed to work with SingleCpuIO): tested in all verif. exp. |
45 |
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o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
46 |
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affects the results (but none of the verification test uses this scheme). |
47 |
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o Adding some pkg/diagnostics capability to pkg/seaice |
48 |
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(will certainly be subject to changes) |
49 |
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o ctrl: adding new control variables: |
50 |
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lwflux, lwdown, evap, snowprecip, apressure, runoff |
51 |
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|
52 |
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checkpoint58q_post |
53 |
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o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
54 |
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1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
55 |
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high_res_cube configuration by 4% on Columbia. |
56 |
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o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
57 |
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add (in global_with_exf/code) a version of EXF_INTERP_READ without |
58 |
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dynamical allocation (seems to work in multi-threaded). |
59 |
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o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
60 |
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single CPU io) so that TAF does not have to see EESUPPORT.h |
61 |
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o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
62 |
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|
63 |
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checkpoint58p_post |
64 |
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o obcs: stop if obcs is used with useCDscheme = .true. |
65 |
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o shelfice: |
66 |
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- fix a sign error so that no slip at shelfice interface works |
67 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
68 |
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not mean, that the results are correct, but at least they are numerically |
69 |
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stable |
70 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
71 |
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o added adjoint exch routined for all exch*3d* routines |
72 |
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and updated flow directives |
73 |
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|
74 |
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checkpoint58o_post |
75 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
76 |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
77 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
78 |
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and clean-up reading/writing of pickup files. |
79 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
80 |
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o simplify EXCH interface: |
81 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
82 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
83 |
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o added the regrid package |
84 |
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o shelfice: |
85 |
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- add a simple boundary layer scheme to reduce noise |
86 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
87 |
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|
88 |
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checkpoint58n_post |
89 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
90 |
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local variable (not in common block). |
91 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
92 |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
93 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
94 |
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to work with SingleCpuIO. |
95 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
96 |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
97 |
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o multi-threading and IO: |
98 |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
99 |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
100 |
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- barrier before and after reading. |
101 |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
102 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
103 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
104 |
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common-block variables ; Allows multi-threading with master-thread IO. |
105 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
106 |
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and stop cleanly when MAX_NO_THREADS is too small. |
107 |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
108 |
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|
109 |
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checkpoint58m_post |
110 |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
111 |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
112 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
113 |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
114 |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
115 |
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o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
116 |
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add MITgcm_tutorials (= code + all the tutorials) |
117 |
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o ecco, option to compute cost for total ssh (mean+anom) |
118 |
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o consistent with addition of ptracer and ssh in pkg/profiles |
119 |
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o profiles: adding ptracer and ssh |
120 |
|
o testreport: change multi-test output-file name |
121 |
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(from output.txt.{name} to output.{name}.txt) |
122 |
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o profiles: now ok for mutli-tiles case |
123 |
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o seaice: add 4 parameters for different advection schemes for area, |
124 |
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(effective) seaice thickness, enthalphy, and snow height. Their default |
125 |
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is the standard parameter SEAICEadvScheme |
126 |
|
o calc_gw: |
127 |
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- add cosFacU in zonal viscous flux (harmonic.visc.). |
128 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
129 |
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of tutorial_plume_on_slope. |
130 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
131 |
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o calc_gw: true flux-form, account for horizontal grid spacing. |
132 |
|
update rotating_tank results, but not plume_on_slope (affected at |
133 |
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truncation level, 11 digits). |
134 |
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|
135 |
|
checkpoint58l_post |
136 |
|
o calc_gw: |
137 |
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- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
138 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
139 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
140 |
|
o commit code to make SST/SSS weights spatially variable |
141 |
|
(based on either variable in-situ or variable initial T/S weights) |
142 |
|
o pkg/ecco: |
143 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
144 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
145 |
|
* cost_averagesflags now returns year indices in addition to day, month |
146 |
|
* sflux balance is performed on annual basis |
147 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
148 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
149 |
|
including separate counting and multipliers |
150 |
|
o pkg/rbcs |
151 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
152 |
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|
153 |
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checkpoint58k_post |
154 |
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o testreport: |
155 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
156 |
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& running in input) |
157 |
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- run in dir run (if it exists), in build otherwise. |
158 |
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- call prepare_run (if input/prepare_run exists) |
159 |
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- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
160 |
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o pkg/exf modifications to interpolation and rotation routines for more |
161 |
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reasonable treatment of North Pole singularity: for tracers North Pole |
162 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
163 |
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set to zero, and for meridional velocity it is set to northernmost value. |
164 |
|
o pkg/exf/exf_check_range.F |
165 |
|
- add tile index to diagnostics and move stop statement to the very |
166 |
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end of the routine. |
167 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
168 |
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define title of isomorphic variables according to the current config. |
169 |
|
o pkg/thsice with pkg/seaice dynamics: |
170 |
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- fix domain of computation (interior only, required for exf) and do exchanges |
171 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
172 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
173 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
174 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
175 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
176 |
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o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
177 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
178 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
179 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
180 |
|
o tracer advection: |
181 |
|
- clean-up and simplify calc_common_factors.F |
182 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
183 |
|
advection subroutine (but still not used within DST advection S/R) |
184 |
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o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
185 |
|
|
186 |
|
checkpoint58j_post |
187 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
188 |
|
from file (collects calls previously in FORWARD_STEP) |
189 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
190 |
|
o adjoint store dir. adjusted accordingly |
191 |
|
o genmake2 |
192 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
193 |
|
|
194 |
|
checkpoint58i_post |
195 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
196 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
197 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
198 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
199 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
200 |
|
on CS-grid: no longer loosing mass. |
201 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
202 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
203 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
204 |
|
- Set to false in order to start EVP solver with |
205 |
|
non-EVP pickup files when using SEAICEuseEVP |
206 |
|
- fix sign error in diffusion in seaice_calc_rhs |
207 |
|
|
208 |
|
checkpoint58h_post |
209 |
|
* Modifications for bottom topography control |
210 |
|
o replace hFacC by _hFacC at various places |
211 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
212 |
|
o add non-self-adjoint cg2d_nsa |
213 |
|
o update autodiff support routines |
214 |
|
o re-initialise hfac after ctrl_depth_ini |
215 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
216 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
217 |
|
|
218 |
|
checkpoint58g_post |
219 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
220 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
221 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
222 |
|
o pkg/ggl90: |
223 |
|
- add parameter (minimum surface kinetic energy) |
224 |
|
- fix bug (avoiding division by zero) |
225 |
|
o couple pkg/thsice to pkg/seaice: |
226 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
227 |
|
- only muliDimAdection scheme work with seaice/thsice |
228 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
229 |
|
- does not break the verification experiments, but does not give the |
230 |
|
desired results either |
231 |
|
o pkg/seaice |
232 |
|
- make (default) second order advection a bit less confusing? |
233 |
|
|
234 |
|
checkpoint58f_post |
235 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
236 |
|
to pkg/seaice): |
237 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
238 |
|
- add an additional formal parameter to thsice_solve4temp |
239 |
|
o pkg/exf: |
240 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
241 |
|
- correct Stefan-Boltzmann constant |
242 |
|
- new parameter for longwave surface emittance |
243 |
|
- separate some stuff from exf_bulkformulae into new routines |
244 |
|
exf_radiation, exf_wind |
245 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
246 |
|
and snow, evaporation parameters over ice |
247 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
248 |
|
either wind from stress or stress from wind |
249 |
|
o pkg/thSIce: |
250 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
251 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
252 |
|
and THSICE_CALC_THICKN |
253 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
254 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
255 |
|
to make debugging easier. |
256 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
257 |
|
o pkg/bulk_force: |
258 |
|
- clean-up comments and parameters ; |
259 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
260 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
261 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
262 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
263 |
|
testreport accordingly |
264 |
|
|
265 |
|
checkpoint58e_post |
266 |
|
o SEAICE_CGRID adjoint done |
267 |
|
o R_STAR adjoint implemented. |
268 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
269 |
|
* need to sort out init. of h0facc, etc. |
270 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
271 |
|
to be able to use it in pure forward. |
272 |
|
|
273 |
|
checkpoint58d_post |
274 |
|
o upgrade simple test-experiment to tutorial example: |
275 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
276 |
|
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
277 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
278 |
|
tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
279 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
280 |
|
tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
281 |
|
tutorial_plume_on_slope <- copy of plume_on_slope |
282 |
|
tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
283 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
284 |
|
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
285 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
286 |
|
o correct a sign problem in cost_scat.F |
287 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
288 |
|
with larger stencil |
289 |
|
o thsice adjoint: start |
290 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
291 |
|
completeness |
292 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
293 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
294 |
|
o ptracers adjoint: |
295 |
|
* avoid extensive recomputatations |
296 |
|
* fix missing re-init. of gptr (missed by TAF) |
297 |
|
o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
298 |
|
me to turn off the excessive output to STDOUT that this package produces |
299 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
300 |
|
and add those terms in Vector-Invariant formulation. |
301 |
|
o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
302 |
|
if the control period (xx_hfluxperiod etc) is 0 |
303 |
|
o in profiles pkg, clean routines and fix details |
304 |
|
o in ecco pkg, reading ssh data: |
305 |
|
fix problem in case the model does not start at iter0=0 |
306 |
|
o fix mnc-pickup/restart for ptracers |
307 |
|
o new package prifiles: |
308 |
|
code to compute profile-based cost by Gael Forget |
309 |
|
(modifs in ecco, ctrl, autodiff) |
310 |
|
o Benign bug fix in initialization (spotted by M. Mazloff) of |
311 |
|
ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
312 |
|
|
313 |
|
checkpoint58c_post |
314 |
|
o adjoint: finish NLFS adjoint and provide reference output in |
315 |
|
verification/global_ocean.90x40x15/results_ad_nlfs |
316 |
|
o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
317 |
|
documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
318 |
|
SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
319 |
|
with SEAICE_CGRID defined. |
320 |
o move calendarDumps from "data" to "data.cal" and clean-up the code |
o move calendarDumps from "data" to "data.cal" and clean-up the code |
321 |
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
322 |
o add useEXF & useCAL flags (for now, set in hard-coded way) |
o add useEXF & useCAL flags (for now, set in hard-coded way) |