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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint58t_post |
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o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
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o pkg/mdsio: |
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- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
11 |
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move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
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mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
13 |
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- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
14 |
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- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
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either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
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- new S/R (to replace MDSWRITEMETA), which allows to write more |
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informations (variable names, time ...) to meta files. |
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- modify rdmds.m to give back the meta file content. |
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o pkg/diagnostics: change vertical interpolation to be safer, and more |
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flexible (define p-levels to interpolate to in data.diagnostics); |
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add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
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diagnostic pointer. |
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o pkg/seaice: more cleaning up of seaice_growth, added many comments |
24 |
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o pkg/exf: put runoff0 and runoff into the appropriate common block |
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o fix multi-category seaice: |
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- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
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SEAICE_MULTICATEGORY |
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- fix short wave heat flux |
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o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
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and allow to use EVP solver. Change forward lab_sea: test both EVP |
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solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
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o Initial check-in of lab_sea adjoint |
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(very similar to natl_box_adjoint/code_seaice) |
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* used C-grid and EVP solver |
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* used KPP, GM/Redi |
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* uses inAdExact=.TRUE. |
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* gradient checks fail for both ADM and TLM |
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due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
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f.d. gradients actually seem more problematic than ADM, TLM gradients; |
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issue is related to forward mismatch between g77 an ifort |
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o pkg/seaice: overhaul of thermodynamics |
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- growth.F and groatb.F are replaced by new routine seaice_growth.F |
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- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
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- move a few global fields out of SEAICE.h into seaice_growth.F and |
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make them 2D (FICE/QNETO/ ...) |
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- remove FO (it is the same as QNETO) |
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- introduce a few local fields to avoid modifying external fields such |
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as atemp, etc. |
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|
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checkpoint58s_post |
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o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
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changed exf_set_gen.F so that |
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genperiod=0 means input file is one time-constant field and |
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genperiod=-12 means input file contains 12 monthly means |
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o CG2D: use pre-computed solver main-diagonal (stored in common block); |
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this affects truncation error ; generate new output file for exp. which |
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fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
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global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
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ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
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MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
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tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
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vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
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o start implementation of deep-atmosphere and anelastic formulation |
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o verification: remove 2nd copy of input files and use script "prepare_run" |
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to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
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o mom_common/vecinv/fluxform: fix a few initialisation isssues |
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o profiles: fix for multithreaded case |
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|
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o diagnostics: rename few diags: |
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s/'PRESSURE'/'RCENTER '/g |
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s/'TICE '/'oceFreez'/g |
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s/'TAUX '/'oceTAUX '/g |
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s/'TAUY '/'oceTAUY '/g |
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s/'SWFLUX '/'oceQsw '/g |
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s/DIFx/DFxE/g |
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s/DIFy/DFyE/g |
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and add few ocean-forcing diagnostics: |
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atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
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o modifications to pkg/seaice/growth.F and budget.F, which change results of |
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lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
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as actual snow thickness. It now refers everywhere to effective snow |
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thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
83 |
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|
84 |
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checkpoint58r_post |
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o modifications to pkg/seaice/growth.F, which change results of |
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lab_sea experiment: fixes pertain to melting snow over open water, to |
87 |
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masking EVAP under sea ice, and to using the correct AREA variable for |
88 |
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computations of EVAP, PRECIP, HSNOW, and GHEFF |
89 |
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o add ability to read bathy, salt, and theta using MNC (off by def) |
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o add flooding algorithm and advection of HSNOW for pkg/seaice; |
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both are turned off by default and do no change any results |
92 |
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o seaice advection with pkg/thsice: a step toward the use of non-linear |
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advection scheme, but #ifdef or commented out for now (requires more EXCH). |
94 |
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o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
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(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
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in natl_box (affects results @ truncation level: update output.txt) |
97 |
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o multi-threading and IO: |
98 |
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- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
99 |
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- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
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(needed to work with SingleCpuIO): tested in all verif. exp. |
101 |
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o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
102 |
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affects the results (but none of the verification test uses this scheme). |
103 |
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o Adding some pkg/diagnostics capability to pkg/seaice |
104 |
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(will certainly be subject to changes) |
105 |
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o ctrl: adding new control variables: |
106 |
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lwflux, lwdown, evap, snowprecip, apressure, runoff |
107 |
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|
108 |
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checkpoint58q_post |
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o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
110 |
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1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
111 |
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high_res_cube configuration by 4% on Columbia. |
112 |
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o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
113 |
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add (in global_with_exf/code) a version of EXF_INTERP_READ without |
114 |
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dynamical allocation (seems to work in multi-threaded). |
115 |
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o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
116 |
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single CPU io) so that TAF does not have to see EESUPPORT.h |
117 |
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o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
118 |
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119 |
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checkpoint58p_post |
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o obcs: stop if obcs is used with useCDscheme = .true. |
121 |
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o shelfice: |
122 |
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- fix a sign error so that no slip at shelfice interface works |
123 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
124 |
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not mean, that the results are correct, but at least they are numerically |
125 |
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stable |
126 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
127 |
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o added adjoint exch routined for all exch*3d* routines |
128 |
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and updated flow directives |
129 |
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|
130 |
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checkpoint58o_post |
131 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
133 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
134 |
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and clean-up reading/writing of pickup files. |
135 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
136 |
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o simplify EXCH interface: |
137 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
138 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
139 |
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o added the regrid package |
140 |
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o shelfice: |
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- add a simple boundary layer scheme to reduce noise |
142 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
143 |
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|
144 |
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checkpoint58n_post |
145 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
146 |
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local variable (not in common block). |
147 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
148 |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
149 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
150 |
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to work with SingleCpuIO. |
151 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
152 |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
153 |
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o multi-threading and IO: |
154 |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
155 |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
156 |
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- barrier before and after reading. |
157 |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
158 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
159 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
160 |
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common-block variables ; Allows multi-threading with master-thread IO. |
161 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
162 |
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and stop cleanly when MAX_NO_THREADS is too small. |
163 |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
164 |
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|
165 |
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checkpoint58m_post |
166 |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
167 |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
168 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
169 |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
170 |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
171 |
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o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
172 |
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add MITgcm_tutorials (= code + all the tutorials) |
173 |
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o ecco, option to compute cost for total ssh (mean+anom) |
174 |
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o consistent with addition of ptracer and ssh in pkg/profiles |
175 |
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o profiles: adding ptracer and ssh |
176 |
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o testreport: change multi-test output-file name |
177 |
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(from output.txt.{name} to output.{name}.txt) |
178 |
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o profiles: now ok for mutli-tiles case |
179 |
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o seaice: add 4 parameters for different advection schemes for area, |
180 |
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(effective) seaice thickness, enthalphy, and snow height. Their default |
181 |
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is the standard parameter SEAICEadvScheme |
182 |
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o calc_gw: |
183 |
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- add cosFacU in zonal viscous flux (harmonic.visc.). |
184 |
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- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
185 |
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of tutorial_plume_on_slope. |
186 |
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o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
187 |
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o calc_gw: true flux-form, account for horizontal grid spacing. |
188 |
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update rotating_tank results, but not plume_on_slope (affected at |
189 |
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truncation level, 11 digits). |
190 |
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|
191 |
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checkpoint58l_post |
192 |
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o calc_gw: |
193 |
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- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
194 |
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- remove side-drag for now (need to fix it); update plume_on_slope results. |
195 |
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- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
196 |
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o commit code to make SST/SSS weights spatially variable |
197 |
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(based on either variable in-situ or variable initial T/S weights) |
198 |
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o pkg/ecco: |
199 |
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* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
200 |
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now based on horizontally varying weights wthetaLev, wsaltLev |
201 |
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* cost_averagesflags now returns year indices in addition to day, month |
202 |
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* sflux balance is performed on annual basis |
203 |
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(sflxumm, sfluxmm2, bal_sfluxmm) |
204 |
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* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
205 |
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including separate counting and multipliers |
206 |
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o pkg/rbcs |
207 |
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* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
208 |
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|
209 |
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checkpoint58k_post |
210 |
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o testreport: |
211 |
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- always build in dir. "build" (if not there, mkdir build instead of building |
212 |
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& running in input) |
213 |
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- run in dir run (if it exists), in build otherwise. |
214 |
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- call prepare_run (if input/prepare_run exists) |
215 |
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- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
216 |
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o pkg/exf modifications to interpolation and rotation routines for more |
217 |
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reasonable treatment of North Pole singularity: for tracers North Pole |
218 |
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value is set to northernmost zonal-mean value, for zonal velocity it is |
219 |
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set to zero, and for meridional velocity it is set to northernmost value. |
220 |
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o pkg/exf/exf_check_range.F |
221 |
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- add tile index to diagnostics and move stop statement to the very |
222 |
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end of the routine. |
223 |
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o pkg/diagnostics: (diagnostics_main_init.F) |
224 |
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define title of isomorphic variables according to the current config. |
225 |
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o pkg/thsice with pkg/seaice dynamics: |
226 |
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- fix domain of computation (interior only, required for exf) and do exchanges |
227 |
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- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
228 |
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o towards a standard way of dealing with multi-threading in MONITOR |
229 |
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and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
230 |
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o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
231 |
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to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
232 |
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o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
233 |
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o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
234 |
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o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
235 |
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(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
236 |
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o tracer advection: |
237 |
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- clean-up and simplify calc_common_factors.F |
238 |
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- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
239 |
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advection subroutine (but still not used within DST advection S/R) |
240 |
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o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
241 |
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|
242 |
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checkpoint58j_post |
243 |
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o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
244 |
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from file (collects calls previously in FORWARD_STEP) |
245 |
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o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
246 |
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o adjoint store dir. adjusted accordingly |
247 |
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o genmake2 |
248 |
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replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
249 |
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|
250 |
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checkpoint58i_post |
251 |
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o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
252 |
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on wind stress (SEAICEstressFactor defaults to 1.) |
253 |
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o Total number of Timers is finite (<=40): comment out 2 non-essential one |
254 |
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in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
255 |
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o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
256 |
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on CS-grid: no longer loosing mass. |
257 |
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o exf & curvilinear-grid: no longer modify longitude xC & xG. |
258 |
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o pkg/ggl90: fix sloppy output and fix a bug |
259 |
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o pkg/seaice: added SEAICEuseEVPpickup parameter |
260 |
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- Set to false in order to start EVP solver with |
261 |
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non-EVP pickup files when using SEAICEuseEVP |
262 |
|
- fix sign error in diffusion in seaice_calc_rhs |
263 |
|
|
264 |
|
checkpoint58h_post |
265 |
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* Modifications for bottom topography control |
266 |
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o replace hFacC by _hFacC at various places |
267 |
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o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
268 |
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o add non-self-adjoint cg2d_nsa |
269 |
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o update autodiff support routines |
270 |
|
o re-initialise hfac after ctrl_depth_ini |
271 |
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o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
272 |
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* Adding verification for 5x5 box (4-layer) bottom topography control |
273 |
|
|
274 |
|
checkpoint58g_post |
275 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
276 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
277 |
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in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
278 |
o pkg/ggl90: |
o pkg/ggl90: |
279 |
- add parameter (minimum surface kinetic energy) |
- add parameter (minimum surface kinetic energy) |
280 |
- fix bug (avoiding division by zero) |
- fix bug (avoiding division by zero) |