4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint59k |
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o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
9 |
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dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
10 |
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o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
11 |
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all experiments pass when compile with un-initilised var. checking option. |
12 |
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o added pkg/salt_plume |
13 |
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o script to test restart (for now, in MITgcm_contrib/jmc_script) |
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o pkg/seaice: new read/write pickup version. |
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read meta file and write only fields which are needed to restart. |
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( same logic as main pickup file ; also using pickupStrictlyMatch ) |
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o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
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o lab_sea.hb87: modify the domain & update output.hb87.txt : |
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lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
20 |
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at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
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process. Fixed here by closing the domain at the Northern boundary. |
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o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
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o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
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a set of consecutive levels in/from a 3-D array. |
25 |
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o pkg/ptracers: |
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use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
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to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
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|
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checkpoint59j |
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o in pkgs: dic, obcs, offline, rbcs: |
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standard way to compute coeff. for time interpolation between 2 time reccords |
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which retains full precision (& make results less dependent on compiler). |
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update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
34 |
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o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
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packages instead of reading ice cover and wind speed separately |
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o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
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(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
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to allow to compile customized code before the update) |
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o cleaning-up: |
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- fix CPP instruction syntax in pkg/obcs |
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- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
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add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
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- fix some threads issue in IO parts. |
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o pkg/dic: |
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- add tons of "_d 0" (--> much better testreports !) |
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and then update outputs of tutorial_global_oce_biogeo |
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o pkg/mom_fluxform: |
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add a special version of momentum advection intended to conserve momentum |
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next to a bathymetry step or a coastline edge. (default = off = #undef) |
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o new read/write pickup version: |
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- for now, only implemented for main (mdsio) pickup file. |
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- write out only what is needed to restart; merge pickup_nh , pickup_ph |
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and main pickup together. |
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- read meta file; read only what is needed to restart; stop if a field |
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is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
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if it make sense (even if the restart is not perfect). |
57 |
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- if no meta file, assume that pickup to read corresponds exactly to |
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a pickup that would currently be written. |
59 |
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- read pickup written in the old format (until checkpoint59i) if it |
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recognizes an old meta file (no field-list). |
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- add a meta file in exp. which starts from a pickup: 2 cases: |
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a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
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e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
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b) a meta file describing the content of the associated pickup file |
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e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
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o pkg/mdsio & pkg/rw: |
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- new routine to read a meta file ; new set of routine to read |
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Multiple-fields file (with meta file). |
69 |
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o added open boundary conditions capability for seaice |
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HSNOW, HSALT, UICE, and VICE |
71 |
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|
72 |
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checkpoint59i |
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o adjoint: |
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* fix multiDimAdvection adjoint |
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(partial recomputation problem by TAF for fVerT(:,:,kDown) |
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and comlev1 size definition (maxpass vs. max. number of tracers) |
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* verification/global_ocean.90x45x15 adjoint now tests |
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NLFS and multiDimAdvection using DST3 (=30) |
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* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
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o pkg/kpp: add "_d 0" to real constant (if missing); |
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update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
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and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
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o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
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for internal parameters related to restart process (formerly from PARAMS.h) |
85 |
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and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
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o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
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as argument. (only atm2d & obcs write_pickup have not yet been updated) |
88 |
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o pkg/monitor: |
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- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
90 |
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- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
91 |
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- account for deep Atmosphere factor and density factor (anelastic) |
92 |
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o added open boundary conditions capability for seaice HEFF and AREA |
93 |
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o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
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thermodynamics |
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- requires a little reorganization, which affects the testreport results |
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of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
97 |
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so that now the conservative form is tested |
98 |
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- add a few comments |
99 |
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o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
100 |
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o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
101 |
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o add new diagnostics to seaice: advective, diffusive fluxes (only for |
102 |
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multidim-advection, for scheme 2 they are not filled) and transports, |
103 |
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thermodynamic growth rates |
104 |
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o change units of EmPmR (inside the code, + within coupling interface) |
105 |
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from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
106 |
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Affects results @ truncation level (cg2d match) and update output of |
107 |
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experiments: lab_sea(6), global_ocean.90x40x15(10), |
108 |
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global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
109 |
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+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
110 |
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Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
111 |
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Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
112 |
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|
113 |
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checkpoint59h |
114 |
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o pkg/exf: |
115 |
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- improve vectorization by moving if-statement out of loops in |
116 |
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exf_mapfields, exf_radiation |
117 |
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- exf_bulkformulae.F: introduce 2D fields and vectorize code |
118 |
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o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
119 |
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o testreport: |
120 |
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- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
121 |
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monitor & update offline_exf_seaice exp. output. |
122 |
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- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
123 |
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o pkg/seaice: |
124 |
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- bug fix in the evp solver: boundary conditions were affected be |
125 |
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masking of zMax/zMin (changes results) |
126 |
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- minor bug fix in boundary conditions in seaice_calc_strainrates |
127 |
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(changes results for no_slip) |
128 |
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- seaice_lsr.F: make interpolation of eta dependent on boundaries |
129 |
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- replace hardcoded lower limit for zeta (zMin) by runtime parameter |
130 |
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- add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean |
131 |
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stress formulation and no-slip boundary conditions |
132 |
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o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP |
133 |
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in gad_calc_rhs.F ; add few safety stops in initialisation phase. |
134 |
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o pkg/seaice: a first HSALT time stepping equation has been checked in |
135 |
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o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV |
136 |
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in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem |
137 |
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without requiring DO-IF statements |
138 |
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o pkg/thsice: |
139 |
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use continuous power-law function for partition of energy between lateral |
140 |
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melting/freezing and thinning/thickening ; old code using step function |
141 |
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still available with #undef THSICE_FRACEN_POWERLAW |
142 |
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update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice |
143 |
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o testreport: change AD testing : check against results/output_adm.txt |
144 |
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using same scripts as for forward test. |
145 |
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|
146 |
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checkpoint59g |
147 |
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o adjoint testing: in preparation for changing testreport: |
148 |
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- output format: cost and grad written on separated lines |
149 |
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- ad output results in directory "results" (instead of "results_ad") |
150 |
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o pkg/seaice: adding ice salinity HSALT as a prognostic variable |
151 |
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o pkg/seaice: changes for using pkg/seaice with pkg/obcs |
152 |
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o pkg/ecco: allow user defined cost function contributions |
153 |
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o testreport: |
154 |
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Allow to choose (per experiment) the list of tested output variables |
155 |
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and the main variable (used to issue a pass/FAIL ) ; |
156 |
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- for now, done by adding the specific list in file: [exp]/input/tr_checklist |
157 |
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- default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ; |
158 |
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Also modify printing of summary: |
159 |
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a) ">" NN "<" indicates the "main" variable (used for pass/FAIL) |
160 |
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b) echo the list of tested variables in the individual summary.txt of |
161 |
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each experiment. |
162 |
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o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of |
163 |
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threads and number of processes (with #define GLOBAL_SUM_SEND_RECV) |
164 |
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(but still depend on the tile decompostion of the domain). |
165 |
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o pkg/seaice: change a discretization detail to make the B-grid code |
166 |
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"more symmetric". This change is likely to remove all "ridges/leads" that |
167 |
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where quasi-aligned with the grid in B-grid solutions. It may also be |
168 |
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the solution to the stress coupling issues with the B-grid. |
169 |
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o each tested exp: add a "run" directory with a standard ".cvsignore" file ; |
170 |
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remove .cvsignore from input dir. (since testreport no longer run here). |
171 |
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o pkg/thsice: |
172 |
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- cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h" |
173 |
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- fix reshaping of sea-ice just after advection: |
174 |
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melt all the ice only if ice-volume is too small. |
175 |
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- re-visit lateral/thinning repartition of melting (modifs from May 04, 2007): |
176 |
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prevent lateral melting if sea-ice fraction is too close to iceMaskMin ; |
177 |
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and update experiment global_ocean.cs32x15.icedyn (+start from pickup files). |
178 |
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o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water |
179 |
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tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged. |
180 |
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o define mass2rUnit & rUnit2mass as units conversion factor, used for surface |
181 |
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forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit |
182 |
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(z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse; |
183 |
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and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error |
184 |
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of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16 |
185 |
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-> update output.txt |
186 |
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o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME): |
187 |
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this affects truncation error: -> update output.txt of exp: |
188 |
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global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr, |
189 |
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ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon. |
190 |
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|
191 |
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checkpoint59f |
192 |
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o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode) |
193 |
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o pkg/ctrl: ctrl_bound forces parameter corrections to stay in |
194 |
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a bounded range (in forward mode) |
195 |
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o pkg/ecco, ctrl, autodiff and mom_common: |
196 |
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internal parameter controls, completements of implementations |
197 |
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o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy. |
198 |
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o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ; |
199 |
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(not seem any difference in testing results). |
200 |
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o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains |
201 |
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at face corners. |
202 |
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o pkg/generic_advdiff: |
203 |
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- in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR) |
204 |
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loop range indices for computing vertical advection tendency |
205 |
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and do the calculation in the interior only (no overlap) ; |
206 |
|
for now, only implemented for SOM advection (to save CPU time). |
207 |
|
- add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment) |
208 |
|
o exch2 adjoint |
209 |
|
First set of changes: |
210 |
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- add exch2 hand-written adjoint templates |
211 |
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- exch2 hand-written no longer use TAF-flag 'nownew_arg' |
212 |
|
This will require cleanup in pkg/autodiff/*.F |
213 |
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(changed routines currently kept separate in verif. code/) |
214 |
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- Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC |
215 |
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that used to hide exch2 or cubed-sphere specific code |
216 |
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(commented via 'cph-exch2') |
217 |
|
o pkg/seaice |
218 |
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- Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE. |
219 |
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o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update |
220 |
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output of global_ocean.cs32x15.thsice . |
221 |
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|
222 |
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checkpoint59e |
223 |
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o exch2: new S/R that only use the cube-tracer (center-position) exchange: |
224 |
|
for B-grid vector (not yet tested) and C-grid vector (<- only used |
225 |
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when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined). |
226 |
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o starting implementation of Duffy et al. (GRL 1999) salt plume scheme |
227 |
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(#ifdef ALLOW_SALT_PLUME) |
228 |
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o gather_2d/scatter_2d: removed halo regions |
229 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
230 |
|
scheme and the corresponding test case (under front_relax dir). For now, |
231 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
232 |
|
adjoint: store directives updated, but gradient checks deteriorated, |
233 |
|
so maybe GM/Redi adjoint is now broken. |
234 |
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o seaice adjoint |
235 |
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* add AREA, HEFF, HSNOW as control variable |
236 |
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(should not change lab_sea results) |
237 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
238 |
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o pkg/seaice: |
239 |
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* added computation of saltFlux in seaice_growth; |
240 |
|
For time being, sea ice salinity is assumed constant |
241 |
|
contribution of snow flooding to freshening of sea ice is neglected. |
242 |
|
SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
243 |
|
defaults to 0.0 in order to maintain backward compatibility. |
244 |
|
Typical values for SEAICE_salinity are 4 to 10 g/kg. |
245 |
|
* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
246 |
|
* added SEAICE_availHeatFrac, which specifies fraction of surface level |
247 |
|
heat content used to melt or grow ice |
248 |
|
* commented out cap of HICE: it helps keep ice thinner |
249 |
|
* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
250 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
251 |
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|
252 |
|
checkpoint59d |
253 |
|
o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
254 |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
255 |
|
(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
256 |
|
o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
257 |
|
and change default value of parameter "GM_Small_Number"; |
258 |
|
update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
259 |
|
global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
260 |
|
tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
261 |
|
o pkg/ecco: cost function when applying pkg/smooth to controls |
262 |
|
o pkg/ctrl: add forcingPrecond run time parameter |
263 |
|
o pkg/seaice: |
264 |
|
- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
265 |
|
- fix bug in metric terms of u-equation in LSR solver (implicit part), |
266 |
|
changes verification/lab_sea |
267 |
|
- rearrange implicit part of u-equation in LSR solver to make it easier to |
268 |
|
read, understand, and debug. This causes changes at the truncation level. |
269 |
|
- fix (serious) bug in the boundary conditions (sign error in the implicit |
270 |
|
part) of the LSR solver. Changes all LSR results. |
271 |
|
- fixed problem with HSNOW initialization to avoid thick snow when AREA |
272 |
|
is initilized with small values - does not change lab_sea results. |
273 |
|
- added HsnowFile initialization capability |
274 |
|
o pkg/smooth: addition to model/src and pkg/ctrl so allow |
275 |
|
initialization of pkg/smooth and application to control vector |
276 |
|
o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
277 |
|
o dependencies: pkg/profiles requires pkg/cal |
278 |
|
o pkg/profiles: |
279 |
|
- added option ALLOW_PROFILES_GENERICGRID |
280 |
|
-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
281 |
|
that interpolation information (grid points and coefficients) is provided |
282 |
|
within the netcdf input files. |
283 |
|
-> sample matlab scripts can be found in MITgcm_contrib/gael |
284 |
|
that allow you to prepare netcdf input files. |
285 |
|
- also modified: cleaner include statements, cleaner error print statements, |
286 |
|
cleaner stops when error, and more tests of the netcdf input files consistency. |
287 |
|
o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
288 |
|
o pkg/seaice: |
289 |
|
- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
290 |
|
requires a new routine: seaice_diagnostics_fill.F |
291 |
|
- make sure that seaice does not move if not forced (pressure replacement |
292 |
|
method, Hibler and Ip, 1995), changes results |
293 |
|
- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
294 |
|
- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
295 |
|
It is turned off by default (=-1.), because it changes the results. |
296 |
|
- make it possible to read AREA from a file, too. |
297 |
|
|
298 |
|
checkpoint59c |
299 |
|
o add S/R and diagnostics for oceanic mixed-layer depth |
300 |
|
o move GMRedi call after all vertical mixing schemes (including KPP) |
301 |
|
o pkg/thsice: |
302 |
|
- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
303 |
|
(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
304 |
|
o pkg/obcs: |
305 |
|
- bug fix for balance code |
306 |
|
o pkg/seaice: |
307 |
|
- allow values of SEAICE_elasticParm > 1 |
308 |
|
- add new parameter SEAICE_evpTauRelax as an alternative |
309 |
|
to SEAICE_elasticParm |
310 |
|
- make lsr boundary conditions free slip (by default), changes result |
311 |
|
- add code for no slip boundary conditions for lsr |
312 |
|
- set minimum of zeta to zero (and not 4e8) (changes results) |
313 |
|
- add a cap on AREA after advecting AREA if seaice_growth is not called |
314 |
|
o change calculation of Visbeck K: |
315 |
|
- no longer depend on tapering scheme; instead, compute slope (limited |
316 |
|
by GM_maxSlope). this is equivalent to what was comuted before with |
317 |
|
clipping or linear tappering. |
318 |
|
- fix vertical averaging (wrong by 1/2 level) |
319 |
|
- leave the old version (but will not be maintained) within |
320 |
|
#ifdef OLD_VISBECK_CALC / #endif |
321 |
|
- update output of exp. ideal_2D_oce |
322 |
|
o change error catch in calc_r_star to improve vectorization |
323 |
|
o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
324 |
|
add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
325 |
|
o adjoint: |
326 |
|
Re-organized adjoint checkpointing according to Matt Mazloff |
327 |
|
(but with modifs/completions/cleanups) |
328 |
|
Storing is now bundled into large arrays to optimized I/O |
329 |
|
(and second step in cleanup of the_main_loop) |
330 |
|
|
331 |
checkpoint59b |
checkpoint59b |
332 |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
333 |
- export/import (between ocean & coupler) fields needed for ocean DIC. |
- export/import (between ocean & coupler) fields needed for ocean DIC. |
380 |
o pkg/thsice: |
o pkg/thsice: |
381 |
fix few little problems, in thsice_calc_thickn.F: |
fix few little problems, in thsice_calc_thickn.F: |
382 |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
- growth vertically (and not laterally) if iceFrac == iceMaskMax |
383 |
- melt laterally only if hIce < hThinIce (as the comments say) |
- melt only laterally if hIce < hThinIce (as the comments say) |
384 |
and in thsice_extend.F: |
and in thsice_extend.F: |
385 |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
386 |
- start to form ice as soon as the minimum ice-volume is reachable. |
- start to form ice as soon as the minimum ice-volume is reachable. |
417 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
418 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
419 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
420 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
421 |
|
are no longer updating the vertical diffusivity array |
422 |
|
(passed as argument) but are (re-) setting those arrays. |
423 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
424 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
425 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |