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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
6 |
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o add ability to read bathy, salt, and theta using MNC (off by def) |
7 |
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o add flooding algorithm and advection of HSNOW for pkg/seaice; |
8 |
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both are turned off by default and do no change any results |
9 |
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o seaice advection with pkg/thsice: a step toward the use of non-linear |
10 |
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advection scheme, but #ifdef or commented out for now (requires more EXCH). |
11 |
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o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
12 |
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(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
13 |
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in natl_box (affects results @ truncation level: update output.txt) |
14 |
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o multi-threading and IO: |
15 |
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- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
16 |
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- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
17 |
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(needed to work with SingleCpuIO): tested in all verif. exp. |
18 |
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o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
19 |
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affects the results (but none of the verification test uses this scheme). |
20 |
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o Adding some pkg/diagnostics capability to pkg/seaice |
21 |
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(will certainly be subject to changes) |
22 |
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o ctrl: adding new control variables: |
23 |
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lwflux, lwdown, evap, snowprecip, apressure, runoff |
24 |
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|
25 |
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checkpoint58q_post |
26 |
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o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
27 |
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1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
28 |
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high_res_cube configuration by 4% on Columbia. |
29 |
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o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
30 |
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add (in global_with_exf/code) a version of EXF_INTERP_READ without |
31 |
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dynamical allocation (seems to work in multi-threaded). |
32 |
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o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
33 |
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single CPU io) so that TAF does not have to see EESUPPORT.h |
34 |
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o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
35 |
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|
36 |
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checkpoint58p_post |
37 |
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o obcs: stop if obcs is used with useCDscheme = .true. |
38 |
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o shelfice: |
39 |
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- fix a sign error so that no slip at shelfice interface works |
40 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
41 |
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not mean, that the results are correct, but at least they are numerically |
42 |
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stable |
43 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
44 |
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o added adjoint exch routined for all exch*3d* routines |
45 |
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and updated flow directives |
46 |
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|
47 |
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checkpoint58o_post |
48 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
49 |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
50 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
51 |
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and clean-up reading/writing of pickup files. |
52 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
53 |
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o simplify EXCH interface: |
54 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
55 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
56 |
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o added the regrid package |
57 |
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o shelfice: |
58 |
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- add a simple boundary layer scheme to reduce noise |
59 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
60 |
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|
61 |
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checkpoint58n_post |
62 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
63 |
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local variable (not in common block). |
64 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
65 |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
66 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
67 |
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to work with SingleCpuIO. |
68 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
69 |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
70 |
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o multi-threading and IO: |
71 |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
72 |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
73 |
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- barrier before and after reading. |
74 |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
75 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
76 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
77 |
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common-block variables ; Allows multi-threading with master-thread IO. |
78 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
79 |
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and stop cleanly when MAX_NO_THREADS is too small. |
80 |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
81 |
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|
82 |
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checkpoint58m_post |
83 |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
84 |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
85 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
86 |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
87 |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
88 |
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o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
89 |
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add MITgcm_tutorials (= code + all the tutorials) |
90 |
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o ecco, option to compute cost for total ssh (mean+anom) |
91 |
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o consistent with addition of ptracer and ssh in pkg/profiles |
92 |
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o profiles: adding ptracer and ssh |
93 |
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o testreport: change multi-test output-file name |
94 |
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(from output.txt.{name} to output.{name}.txt) |
95 |
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o profiles: now ok for mutli-tiles case |
96 |
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o seaice: add 4 parameters for different advection schemes for area, |
97 |
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(effective) seaice thickness, enthalphy, and snow height. Their default |
98 |
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is the standard parameter SEAICEadvScheme |
99 |
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o calc_gw: |
100 |
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- add cosFacU in zonal viscous flux (harmonic.visc.). |
101 |
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- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
102 |
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of tutorial_plume_on_slope. |
103 |
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o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
104 |
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o calc_gw: true flux-form, account for horizontal grid spacing. |
105 |
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update rotating_tank results, but not plume_on_slope (affected at |
106 |
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truncation level, 11 digits). |
107 |
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|
108 |
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checkpoint58l_post |
109 |
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o calc_gw: |
110 |
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- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
111 |
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- remove side-drag for now (need to fix it); update plume_on_slope results. |
112 |
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- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
113 |
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o commit code to make SST/SSS weights spatially variable |
114 |
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(based on either variable in-situ or variable initial T/S weights) |
115 |
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o pkg/ecco: |
116 |
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* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
117 |
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now based on horizontally varying weights wthetaLev, wsaltLev |
118 |
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* cost_averagesflags now returns year indices in addition to day, month |
119 |
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* sflux balance is performed on annual basis |
120 |
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(sflxumm, sfluxmm2, bal_sfluxmm) |
121 |
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* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
122 |
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including separate counting and multipliers |
123 |
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o pkg/rbcs |
124 |
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* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
125 |
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126 |
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checkpoint58k_post |
127 |
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o testreport: |
128 |
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- always build in dir. "build" (if not there, mkdir build instead of building |
129 |
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& running in input) |
130 |
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- run in dir run (if it exists), in build otherwise. |
131 |
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- call prepare_run (if input/prepare_run exists) |
132 |
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- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
133 |
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o pkg/exf modifications to interpolation and rotation routines for more |
134 |
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reasonable treatment of North Pole singularity: for tracers North Pole |
135 |
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value is set to northernmost zonal-mean value, for zonal velocity it is |
136 |
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set to zero, and for meridional velocity it is set to northernmost value. |
137 |
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o pkg/exf/exf_check_range.F |
138 |
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- add tile index to diagnostics and move stop statement to the very |
139 |
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end of the routine. |
140 |
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o pkg/diagnostics: (diagnostics_main_init.F) |
141 |
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define title of isomorphic variables according to the current config. |
142 |
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o pkg/thsice with pkg/seaice dynamics: |
143 |
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- fix domain of computation (interior only, required for exf) and do exchanges |
144 |
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- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
145 |
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o towards a standard way of dealing with multi-threading in MONITOR |
146 |
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and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
147 |
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o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
148 |
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to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
149 |
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o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
150 |
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o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
151 |
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o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
152 |
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(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
153 |
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o tracer advection: |
154 |
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- clean-up and simplify calc_common_factors.F |
155 |
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- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
156 |
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advection subroutine (but still not used within DST advection S/R) |
157 |
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o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
158 |
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|
159 |
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checkpoint58j_post |
160 |
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o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
161 |
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from file (collects calls previously in FORWARD_STEP) |
162 |
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o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
163 |
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o adjoint store dir. adjusted accordingly |
164 |
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o genmake2 |
165 |
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replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
166 |
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|
167 |
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checkpoint58i_post |
168 |
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o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
169 |
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on wind stress (SEAICEstressFactor defaults to 1.) |
170 |
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o Total number of Timers is finite (<=40): comment out 2 non-essential one |
171 |
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in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
172 |
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o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
173 |
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on CS-grid: no longer loosing mass. |
174 |
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o exf & curvilinear-grid: no longer modify longitude xC & xG. |
175 |
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o pkg/ggl90: fix sloppy output and fix a bug |
176 |
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o pkg/seaice: added SEAICEuseEVPpickup parameter |
177 |
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- Set to false in order to start EVP solver with |
178 |
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non-EVP pickup files when using SEAICEuseEVP |
179 |
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- fix sign error in diffusion in seaice_calc_rhs |
180 |
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|
181 |
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checkpoint58h_post |
182 |
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* Modifications for bottom topography control |
183 |
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o replace hFacC by _hFacC at various places |
184 |
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o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
185 |
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o add non-self-adjoint cg2d_nsa |
186 |
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o update autodiff support routines |
187 |
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o re-initialise hfac after ctrl_depth_ini |
188 |
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o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
189 |
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* Adding verification for 5x5 box (4-layer) bottom topography control |
190 |
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|
191 |
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checkpoint58g_post |
192 |
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o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
193 |
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used for mean seasonal cycle, mean diurnal cycle); add an example |
194 |
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in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
195 |
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o pkg/ggl90: |
196 |
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- add parameter (minimum surface kinetic energy) |
197 |
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- fix bug (avoiding division by zero) |
198 |
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o couple pkg/thsice to pkg/seaice: |
199 |
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- modify advection in seaice to accomodate new scalar fields to be advected |
200 |
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- only muliDimAdection scheme work with seaice/thsice |
201 |
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- mapping of thsice-variables to seaice-variables, back and forth |
202 |
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- does not break the verification experiments, but does not give the |
203 |
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desired results either |
204 |
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o pkg/seaice |
205 |
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- make (default) second order advection a bit less confusing? |
206 |
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|
207 |
|
checkpoint58f_post |
208 |
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o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
209 |
|
to pkg/seaice): |
210 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
211 |
|
- add an additional formal parameter to thsice_solve4temp |
212 |
|
o pkg/exf: |
213 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
214 |
|
- correct Stefan-Boltzmann constant |
215 |
|
- new parameter for longwave surface emittance |
216 |
|
- separate some stuff from exf_bulkformulae into new routines |
217 |
|
exf_radiation, exf_wind |
218 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
219 |
|
and snow, evaporation parameters over ice |
220 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
221 |
|
either wind from stress or stress from wind |
222 |
|
o pkg/thSIce: |
223 |
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- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
224 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
225 |
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and THSICE_CALC_THICKN |
226 |
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- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
227 |
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- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
228 |
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to make debugging easier. |
229 |
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- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
230 |
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o pkg/bulk_force: |
231 |
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- clean-up comments and parameters ; |
232 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
233 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
234 |
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generate new output for test-experiment: aim.5l_cs.thSI |
235 |
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o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
236 |
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testreport accordingly |
237 |
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|
238 |
|
checkpoint58e_post |
239 |
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o SEAICE_CGRID adjoint done |
240 |
|
o R_STAR adjoint implemented. |
241 |
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* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
242 |
|
* need to sort out init. of h0facc, etc. |
243 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
244 |
|
to be able to use it in pure forward. |
245 |
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|
246 |
|
checkpoint58d_post |
247 |
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o upgrade simple test-experiment to tutorial example: |
248 |
|
step.1: duplicate the experiment and (step.2) will remove the old copy. |
249 |
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tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
250 |
|
tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
251 |
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tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
252 |
|
tutorial_global_oce_biogeo <- copy of dic_example |
253 |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
254 |
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tutorial_plume_on_slope <- copy of plume_on_slope |
255 |
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tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
256 |
|
tutorial_global_oce_optim <- empty for now (David ?) |
257 |
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tutorial_global_oce_in_p <- copy of global_ocean_pressure |
258 |
|
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
259 |
|
o correct a sign problem in cost_scat.F |
260 |
|
o obcs and ptracers: fix boundary conditions for advections schemes |
261 |
|
with larger stencil |
262 |
|
o thsice adjoint: start |
263 |
|
o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
264 |
|
completeness |
265 |
|
o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
266 |
|
and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
267 |
o ptracers adjoint: |
o ptracers adjoint: |
268 |
* avoid extensive recomputatations |
* avoid extensive recomputatations |
269 |
* fix missing re-init. of gptr (missed by TAF) |
* fix missing re-init. of gptr (missed by TAF) |