4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o gather_2d/scatter_2d: removed halo regions |
8 |
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o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007 |
9 |
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scheme and the corresponding test case (under front_relax dir). For now, |
10 |
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only available with Skew-flux form and not yet tested in realistic set-up. |
11 |
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adjoint: store directives updated, but gradient checks deteriorated, |
12 |
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so maybe GM/Redi adjoint is now broken. |
13 |
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o seaice adjoint |
14 |
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* add AREA, HEFF, HSNOW as control variable |
15 |
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(should not change lab_sea results) |
16 |
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* CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40 |
17 |
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o pkg/seaice: |
18 |
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* added computation of saltFlux in seaice_growth; |
19 |
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For time being, sea ice salinity is assumed constant |
20 |
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contribution of snow flooding to freshening of sea ice is neglected. |
21 |
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SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it |
22 |
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defaults to 0.0 in order to maintain backward compatibility. |
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Typical values for SEAICE_salinity are 4 to 10 g/kg. |
24 |
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* replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F |
25 |
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* added SEAICE_availHeatFrac, which specifies fraction of surface level |
26 |
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heat content used to melt or grow ice |
27 |
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* commented out cap of HICE: it helps keep ice thinner |
28 |
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* reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option |
29 |
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* applied OBCS T/S mask to HEFFM sea ice mask |
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|
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checkpoint59d |
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o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array |
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for {PKG} state variables, and called from DO_STATEVARS_DIAGS. |
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(keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics) |
35 |
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o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0" |
36 |
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and change default value of parameter "GM_Small_Number"; |
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update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15, |
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global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf, |
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tutorial_global_oce_biogeo, tutorial_global_oce_latlon |
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o pkg/ecco: cost function when applying pkg/smooth to controls |
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o pkg/ctrl: add forcingPrecond run time parameter |
42 |
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o pkg/seaice: |
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- replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code |
44 |
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- fix bug in metric terms of u-equation in LSR solver (implicit part), |
45 |
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changes verification/lab_sea |
46 |
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- rearrange implicit part of u-equation in LSR solver to make it easier to |
47 |
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read, understand, and debug. This causes changes at the truncation level. |
48 |
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- fix (serious) bug in the boundary conditions (sign error in the implicit |
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part) of the LSR solver. Changes all LSR results. |
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- fixed problem with HSNOW initialization to avoid thick snow when AREA |
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is initilized with small values - does not change lab_sea results. |
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- added HsnowFile initialization capability |
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o pkg/smooth: addition to model/src and pkg/ctrl so allow |
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initialization of pkg/smooth and application to control vector |
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o pkg/seaice: fix another bug in the LSR no-slip boundary conditons |
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o dependencies: pkg/profiles requires pkg/cal |
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o pkg/profiles: |
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- added option ALLOW_PROFILES_GENERICGRID |
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-> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming |
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that interpolation information (grid points and coefficients) is provided |
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within the netcdf input files. |
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-> sample matlab scripts can be found in MITgcm_contrib/gael |
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that allow you to prepare netcdf input files. |
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- also modified: cleaner include statements, cleaner error print statements, |
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cleaner stops when error, and more tests of the netcdf input files consistency. |
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o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs. |
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o pkg/seaice: |
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- move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this |
69 |
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requires a new routine: seaice_diagnostics_fill.F |
70 |
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- make sure that seaice does not move if not forced (pressure replacement |
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method, Hibler and Ip, 1995), changes results |
72 |
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- and new damping criterion for EVP solver according to Hunke, JCP, 2001 |
73 |
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- SEAICE_evpDampC = > 0. turns it on (615. is the recommended value). |
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It is turned off by default (=-1.), because it changes the results. |
75 |
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- make it possible to read AREA from a file, too. |
76 |
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|
77 |
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checkpoint59c |
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o add S/R and diagnostics for oceanic mixed-layer depth |
79 |
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o move GMRedi call after all vertical mixing schemes (including KPP) |
80 |
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o pkg/thsice: |
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- ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs |
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(melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice |
83 |
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o pkg/obcs: |
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- bug fix for balance code |
85 |
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o pkg/seaice: |
86 |
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- allow values of SEAICE_elasticParm > 1 |
87 |
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- add new parameter SEAICE_evpTauRelax as an alternative |
88 |
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to SEAICE_elasticParm |
89 |
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- make lsr boundary conditions free slip (by default), changes result |
90 |
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- add code for no slip boundary conditions for lsr |
91 |
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- set minimum of zeta to zero (and not 4e8) (changes results) |
92 |
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- add a cap on AREA after advecting AREA if seaice_growth is not called |
93 |
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o change calculation of Visbeck K: |
94 |
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- no longer depend on tapering scheme; instead, compute slope (limited |
95 |
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by GM_maxSlope). this is equivalent to what was comuted before with |
96 |
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clipping or linear tappering. |
97 |
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- fix vertical averaging (wrong by 1/2 level) |
98 |
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- leave the old version (but will not be maintained) within |
99 |
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#ifdef OLD_VISBECK_CALC / #endif |
100 |
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- update output of exp. ideal_2D_oce |
101 |
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o change error catch in calc_r_star to improve vectorization |
102 |
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o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and |
103 |
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add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf). |
104 |
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o adjoint: |
105 |
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Re-organized adjoint checkpointing according to Matt Mazloff |
106 |
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(but with modifs/completions/cleanups) |
107 |
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Storing is now bundled into large arrays to optimized I/O |
108 |
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(and second step in cleanup of the_main_loop) |
109 |
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|
110 |
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checkpoint59b |
111 |
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o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d): |
112 |
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- export/import (between ocean & coupler) fields needed for ocean DIC. |
113 |
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o pkg/seaice: |
114 |
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- get rid of three more exchanges seaice_calc_viscosities (required |
115 |
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different loop boundaries in seaice_lsr and seaice_ocean_stress) |
116 |
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- bug fix in seaice_ocean_stress (update of lab_sea required) |
117 |
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- reduce loop boundaries to necessary minimum also in seaice_evp |
118 |
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- go back to the old way of computing deltaC/Z as the adjoint likes that |
119 |
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better |
120 |
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o Refresh of tutorial_global_oce_latlon (includes changing salinity-like |
121 |
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passive tracer to an Age Tracer) + update output.txt |
122 |
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o pkg/exf: |
123 |
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- implement A-grid / C-grid selection for wind-stress input files. |
124 |
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- clean-up exf_wind.F (remove us, use wspeed instead ; add wStress) |
125 |
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for now, in exf_bulk_largeyeager04.F only : |
126 |
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- change implementation for case where windspeed + 2. components wind-stress |
127 |
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are read-in. AND use rhoConstFresh to convert evap. |
128 |
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o pkg/seaice: |
129 |
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- use correct EXCH_UV for wind-forcing (on A-grid). |
130 |
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- change SEAICE_OPTIONS.h to limit the number of option combinations (regarding |
131 |
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SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops. |
132 |
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o pkg/exf: |
133 |
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- default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC) |
134 |
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EXF_INTERPOLATION: |
135 |
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- merge global_with_exf/code version of exf_interp_read.F |
136 |
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to the main code ; |
137 |
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- Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when |
138 |
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reading the file ; Important: This options needs to be defined to recover |
139 |
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previous code. |
140 |
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otherwise, use fixed size array to read in (size=exf_interp_bufferSize). |
141 |
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- no longer loose real*8 precision along the way when using exf_iprec=64. |
142 |
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o pkg/seaice: rearrangement of common blocks (really needs more cleaning up) |
143 |
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- change discretisation of evp-solver in order to avoid another exchange |
144 |
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(changes lab_sea) and clean up a little |
145 |
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- replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS) |
146 |
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help the adjoint (this also changes the results slightly) |
147 |
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- add a few "_d 0" where they had been missing in seaice_evp.F |
148 |
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- cleaning up: remove unused seaice_calc_rhs.F |
149 |
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o pkg/exf: some cleaning-up: |
150 |
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- change various "constants" into runtime parameters |
151 |
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- cleaned-up Large&Yeager04 routine which should eventually |
152 |
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replace exf_bulkformulae.F (changed names of S/R and CPP) |
153 |
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and merged various ALLOW_ATM_WIND options |
154 |
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only used with thsice pkg (in thsice_get_exf.F): |
155 |
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- implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04) |
156 |
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which are used when useStabilityFct_overIce=TRUE (= the default) |
157 |
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- change default values of ice & snow emissivity and scale downward LW |
158 |
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by ice & snow emissivity. |
159 |
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o pkg/thsice: |
160 |
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fix few little problems, in thsice_calc_thickn.F: |
161 |
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- growth vertically (and not laterally) if iceFrac == iceMaskMax |
162 |
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- melt only laterally if hIce < hThinIce (as the comments say) |
163 |
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and in thsice_extend.F: |
164 |
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- allow to form ice even when iceFrac == iceMaskMax (by increasing thickness) |
165 |
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- start to form ice as soon as the minimum ice-volume is reachable. |
166 |
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update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice), |
167 |
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and cpl_aim+ocn |
168 |
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o pkg/kpp |
169 |
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- move computation of surface related input fields to KPP into a new |
170 |
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subroutine kpp_forcing_surf.F |
171 |
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- remove wrong (within bi,bj loops) EXCH calls. |
172 |
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- little cleaning (add argument myThid in last position, cvs header ...) |
173 |
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- for now, fix conservation problem by exchanging KPPviscAz (may not |
174 |
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be the best fix) |
175 |
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o pkg/seaice |
176 |
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- check for inconsistent evp parameter/cpp-flag combination |
177 |
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- remove leftover errIO flat for obsolete name list error handling |
178 |
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o OpenAD |
179 |
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- changed verification/OpenAD to full baroclinic setup (including GM/Redi) |
180 |
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|
181 |
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checkpoint59a |
182 |
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o pkg/seaice: some parameter clarifications and a little bit of clean up |
183 |
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o pkg/thsice: rename run-time parameters: |
184 |
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himin -> hIceMin |
185 |
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himin0 -> hThinIce |
186 |
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hihig -> hThickIce |
187 |
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i0 -> i0swFrac |
188 |
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transCoef -> bMeltCoef |
189 |
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frac_energy -> fracMelting |
190 |
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add new parameters: hNewIceMax, fracFreezing, dhSnowLin |
191 |
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with default values (for now) that do not change the results. |
192 |
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remove old version of thsice vars advection in pkg/seaice. |
193 |
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o in FFIELDS.h: |
194 |
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- replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD |
195 |
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- make pLoad & sIceLoad always available (but still only used if |
196 |
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ATMOSPHERIC_LOADING is #define). |
197 |
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o pkg/kpp: replaced _KPP_RL with _RL |
198 |
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o bug fixes for vertical diffusivity computations when both KPP and |
199 |
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3D diffusivity arrays are used. |
200 |
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o pkg/seaice: fix bug in evp solver, while doing that |
201 |
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- change (improve?) discretization of stress computations for both |
202 |
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cgrid-lsr and evp solver |
203 |
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- add a new routine to compute strain rates |
204 |
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- the above changes lab_sea results |
205 |
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- add no slip conditions for evp solver (off by default), lsr-version |
206 |
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may follow |
207 |
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- fix exchange for shear at Z-points (does not change lab_sea) |
208 |
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- retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp |
209 |
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(to force the user to pick a time step since there is not "safe" way |
210 |
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of choosing it) |
211 |
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- add principal stress diagnostics |
212 |
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- rearrange fields for evp a little to avoid having to call a: too many |
213 |
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exchanges and b: exchanges for stress trensor components which we do |
214 |
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not have. |
215 |
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- modify Hibler+Bryan (1987) stress coupling so that it reuses information |
216 |
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of evp, complete rewrite for lsr case (latter is does not yet work |
217 |
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in all cases) |
218 |
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o pkg/kpp: add code to have mixing in shelf ice caverns |
219 |
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- add myThid to all kpp routines (long overdue) |
220 |
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|
221 |
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checkpoint59 |
222 |
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o pkg/exf: |
223 |
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- fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND & |
224 |
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ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid |
225 |
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- move exf header files from lower_case.h to UPPER_CASE.h ; |
226 |
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add missing cvs Header & Name |
227 |
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- add adjoint routines and flow dirs for newly used exch_uv_agrid routines |
228 |
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- add namelist param. selectStressGridPosition, exf_monFreq |
229 |
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- retire many _CLIM routines, and remove data.exf_clim |
230 |
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+ params moved to data.exf |
231 |
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+ climsst, climsss now handled by exf_set_gen, i.e. |
232 |
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climss?period=0 refers to constant field, |
233 |
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climss?period=-12 to monthly forcing |
234 |
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- split up namelists in data.exf |
235 |
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o pkg/seaice: |
236 |
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- remove seaice_exch and seaice_exch_uv |
237 |
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- remove superfluous exchange of theta |
238 |
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- add myThid to seaice_budget_ocean/ice |
239 |
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- add new interface for atmospheric wind forcing (C-grid only) |
240 |
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+ new routine |
241 |
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+ two new field (taux, tauy for stress over ice) |
242 |
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+ removed one global field (DAIRN) for C-grid case only |
243 |
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o pkg/thsise |
244 |
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- 2nd set of modifs for thsice adjoint in conjunction with exf |
245 |
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o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.) |
246 |
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|
247 |
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checkpoint58y_post |
248 |
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o Added capability for latitudinal dependence of Bryan and Lewis, 1979 |
249 |
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vertical diffusivity, similar to that in MOM4; turned on using |
250 |
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#define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using |
251 |
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diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file. |
252 |
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o Added capability for 3D specification of background vertical diffusion |
253 |
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coefficient. This is done by (i) #define ALLOW_3D_DIFFKR |
254 |
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in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime |
255 |
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"data" file that contains the 3D vertical diffusivity coefficients. |
256 |
|
o ice dynamics (pkg/seaice) with thsice thermodynamics: |
257 |
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- add code within pkg thsice to advect & diffuse sea-ice fields |
258 |
|
similar to (and will replace) what has been added in seaice_advdiff.F, |
259 |
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but: - conserving Mass, Heat & Salt. |
260 |
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- better when using non-linear advection scheme (not yet fully tested) |
261 |
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- can also be used in atmospheric set-up (for now, only the diffusion). |
262 |
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|
263 |
|
checkpoint58x_post |
264 |
|
o IO option for global-file compact format: |
265 |
|
- add options when generating topology (utils/exch2/matlab-topology-generator) |
266 |
|
- add I/O capability (pkg/mdsio). |
267 |
|
- adapt utils/matlab/rdmds.m to read this format. |
268 |
|
for now long-line format not yet supported by pkg/mdsio (& exch2). |
269 |
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o shelfice: add a few diagnostics |
270 |
|
|
271 |
|
checkpoint58w_post |
272 |
|
o p-coord. non-hydrostatic using reference profile for w <-> omega conversion: |
273 |
|
rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref |
274 |
|
(and replace horiVertRatio in NH code). |
275 |
|
Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !) |
276 |
|
and tutorial_plume_on_slope (sensitive to truncation) |
277 |
|
o seaice: if ALLOW_ATM_WIND is undefined use wind stress |
278 |
|
directly to drive seaice model (C-grid only) |
279 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND): |
280 |
|
- reintroduce computation of wind from stress, |
281 |
|
- compute tau (in exf_bulkformulae.F) from windstress averaged to |
282 |
|
mass points to avoid tau = 0 |
283 |
|
- fix serious bug: (1/3) in Fortran is not the same as (1./3.) |
284 |
|
o rdmnc.m: make it work with "global" files created with gluemnc |
285 |
|
o rdmnc.m : some improvements in dealing with singleton dimension |
286 |
|
(tested on all testreport mnc output files). |
287 |
|
o genmake2: disable pkg/profiles if netcdf test fails. |
288 |
|
o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output. |
289 |
|
o move call to cal_readparms up to make calendar parameters/variable available |
290 |
|
to all packages |
291 |
|
|
292 |
|
checkpoint58v_post |
293 |
|
o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get |
294 |
|
useDynP_inEos_Zc tested. |
295 |
|
o pkg/exf: changes to properly interpolate/mask/scale initial fields |
296 |
|
o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields |
297 |
|
and portions thereof. See read_cs.txt for description and examples. |
298 |
|
o utils/matlab/cs_grid/bk_line: to compute transport through passages, |
299 |
|
add a script (grt_circ_bkl.m) to generate broken-line between 2 points, |
300 |
|
following the great-circle arc between those 2 points. |
301 |
|
o trap un-initialized variable with pathscale compiler on weddell.mit.edu |
302 |
|
(thanks to Constantinos): fix few problems and get (almost) all exp to pass. |
303 |
|
o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in |
304 |
|
- enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h) |
305 |
|
- used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81) |
306 |
|
- still needs work (not working with some options ; efficiency to improve) |
307 |
|
and serious testing. |
308 |
|
- use this scheme for temperature & salinity in 2 advection test exp.: |
309 |
|
advect_xy & advect_xz, respectively. |
310 |
|
|
311 |
|
checkpoint58u_post |
312 |
|
o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels. |
313 |
|
o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA. |
314 |
|
o testreport: add option "-skipdir" to skip some test. |
315 |
|
o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent |
316 |
|
momentum calculation. |
317 |
|
o gad_advection: fix vertAdvecScheme (if different from advectionScheme) |
318 |
|
o some cleaning: usePickupBeforeC35 no longer supported ; remove this option. |
319 |
|
remove checkpoint.F and the_correction_step.F (no longer used); |
320 |
|
do the k loop inside CYCLE_TRACER (supposed to be more efficient). |
321 |
|
o add option (linFSConserveTr) to correct for tracer source/sink due to |
322 |
|
Linear Free surface |
323 |
|
o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine |
324 |
|
o pkg/thsice: fix reading mnc-pickups |
325 |
|
|
326 |
|
checkpoint58t_post |
327 |
|
o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F) |
328 |
|
o pkg/mdsio: |
329 |
|
- clean-up mdsio_readfield.F & mdsio_writefield_new.F and |
330 |
|
move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) & |
331 |
|
mdsio_write_field.F (S/R MDS_WRITE_FIELD); |
332 |
|
- fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD |
333 |
|
- collect old S/R in one file: mdsio_rw_field.F (now just a call to |
334 |
|
either MDS_READ_FIELD or MDS_WRITE_FIELD ) |
335 |
|
- new S/R (to replace MDSWRITEMETA), which allows to write more |
336 |
|
informations (variable names, time ...) to meta files. |
337 |
|
- modify rdmds.m to give back the meta file content. |
338 |
|
o pkg/diagnostics: change vertical interpolation to be safer, and more |
339 |
|
flexible (define p-levels to interpolate to in data.diagnostics); |
340 |
|
add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right |
341 |
|
diagnostic pointer. |
342 |
|
o pkg/seaice: more cleaning up of seaice_growth, added many comments |
343 |
|
o pkg/exf: put runoff0 and runoff1 into the appropriate common block |
344 |
|
o fix multi-category seaice: |
345 |
|
- change cpp flag SEAICE_MULTILEVEL to more meaningful name: |
346 |
|
SEAICE_MULTICATEGORY |
347 |
|
- fix short wave heat flux |
348 |
|
o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics |
349 |
|
and allow to use EVP solver. Change forward lab_sea: test both EVP |
350 |
|
solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint) |
351 |
|
o Initial check-in of lab_sea adjoint |
352 |
|
(very similar to natl_box_adjoint/code_seaice) |
353 |
|
* used C-grid and EVP solver |
354 |
|
* used KPP, GM/Redi |
355 |
|
* uses inAdExact=.TRUE. |
356 |
|
* gradient checks fail for both ADM and TLM |
357 |
|
due to sensitive snow melt code in seaice_grwoth (look for "JZ") |
358 |
|
f.d. gradients actually seem more problematic than ADM, TLM gradients; |
359 |
|
issue is related to forward mismatch between g77 an ifort |
360 |
|
o pkg/seaice: overhaul of thermodynamics |
361 |
|
- growth.F and groatb.F are replaced by new routine seaice_growth.F |
362 |
|
- budget.F is replaced by two new routines seaice_budget_ocean/ice.F |
363 |
|
- move a few global fields out of SEAICE.h into seaice_growth.F and |
364 |
|
make them 2D (FICE/QNETO/ ...) |
365 |
|
- remove FO (it is the same as QNETO) |
366 |
|
- introduce a few local fields to avoid modifying external fields such |
367 |
|
as atemp, etc. |
368 |
|
|
369 |
|
checkpoint58s_post |
370 |
|
o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F |
371 |
|
changed exf_set_gen.F so that |
372 |
|
genperiod=0 means input file is one time-constant field and |
373 |
|
genperiod=-12 means input file contains 12 monthly means |
374 |
|
o CG2D: use pre-computed solver main-diagonal (stored in common block); |
375 |
|
this affects truncation error ; generate new output file for exp. which |
376 |
|
fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d), |
377 |
|
global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d), |
378 |
|
ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d), |
379 |
|
MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d), |
380 |
|
tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d), |
381 |
|
vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d) |
382 |
|
o start implementation of deep-atmosphere and anelastic formulation |
383 |
|
o verification: remove 2nd copy of input files and use script "prepare_run" |
384 |
|
to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M) |
385 |
|
o mom_common/vecinv/fluxform: fix a few initialisation isssues |
386 |
|
o profiles: fix for multithreaded case |
387 |
|
|
388 |
|
o diagnostics: rename few diags: |
389 |
|
s/'PRESSURE'/'RCENTER '/g |
390 |
|
s/'TICE '/'oceFreez'/g |
391 |
|
s/'TAUX '/'oceTAUX '/g |
392 |
|
s/'TAUY '/'oceTAUY '/g |
393 |
|
s/'SWFLUX '/'oceQsw '/g |
394 |
|
s/DIFx/DFxE/g |
395 |
|
s/DIFy/DFyE/g |
396 |
|
and add few ocean-forcing diagnostics: |
397 |
|
atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS |
398 |
|
o modifications to pkg/seaice/growth.F and budget.F, which change results of |
399 |
|
lab_sea experiment: HSNOW was sometimes treated as effective and sometimes |
400 |
|
as actual snow thickness. It now refers everywhere to effective snow |
401 |
|
thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA. |
402 |
|
|
403 |
|
checkpoint58r_post |
404 |
|
o modifications to pkg/seaice/growth.F, which change results of |
405 |
|
lab_sea experiment: fixes pertain to melting snow over open water, to |
406 |
|
masking EVAP under sea ice, and to using the correct AREA variable for |
407 |
|
computations of EVAP, PRECIP, HSNOW, and GHEFF |
408 |
|
o add ability to read bathy, salt, and theta using MNC (off by def) |
409 |
|
o add flooding algorithm and advection of HSNOW for pkg/seaice; |
410 |
|
both are turned off by default and do no change any results |
411 |
|
o seaice advection with pkg/thsice: a step toward the use of non-linear |
412 |
|
advection scheme, but #ifdef or commented out for now (requires more EXCH). |
413 |
|
o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens |
414 |
|
(identical results) and the standard version of EXTERNAL_FIELDS_LOAD |
415 |
|
in natl_box (affects results @ truncation level: update output.txt) |
416 |
|
o multi-threading and IO: |
417 |
|
- replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R. |
418 |
|
- remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls |
419 |
|
(needed to work with SingleCpuIO): tested in all verif. exp. |
420 |
|
o GAD: use simpler DST3 formulation as default (old version left within #ifdef) |
421 |
|
affects the results (but none of the verification test uses this scheme). |
422 |
|
o Adding some pkg/diagnostics capability to pkg/seaice |
423 |
|
(will certainly be subject to changes) |
424 |
|
o ctrl: adding new control variables: |
425 |
|
lwflux, lwdown, evap, snowprecip, apressure, runoff |
426 |
|
|
427 |
|
checkpoint58q_post |
428 |
|
o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up |
429 |
|
1/6-deg Southern Ocean configuration by 8% on IBM Datastar and |
430 |
|
high_res_cube configuration by 4% on Columbia. |
431 |
|
o clean-up multi-threaded problems (reported by debugger tcheck on ACES); |
432 |
|
add (in global_with_exf/code) a version of EXF_INTERP_READ without |
433 |
|
dynamical allocation (seems to work in multi-threaded). |
434 |
|
o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using |
435 |
|
single CPU io) so that TAF does not have to see EESUPPORT.h |
436 |
|
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
437 |
|
|
438 |
|
checkpoint58p_post |
439 |
|
o obcs: stop if obcs is used with useCDscheme = .true. |
440 |
|
o shelfice: |
441 |
|
- fix a sign error so that no slip at shelfice interface works |
442 |
|
- remove stop for combination non-hydrostatic code and shelfice. That does |
443 |
|
not mean, that the results are correct, but at least they are numerically |
444 |
|
stable |
445 |
|
o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
446 |
|
o added adjoint exch routined for all exch*3d* routines |
447 |
|
and updated flow directives |
448 |
|
|
449 |
|
checkpoint58o_post |
450 |
|
o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
451 |
|
remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
452 |
|
o change controling S/R for writing pickup file (new S/R do_write_pickup) |
453 |
|
and clean-up reading/writing of pickup files. |
454 |
|
o fix local version of read/write pickup (NH part) in rotating_tank/code |
455 |
|
o simplify EXCH interface: |
456 |
|
- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
457 |
|
- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
458 |
|
o added the regrid package |
459 |
|
o shelfice: |
460 |
|
- add a simple boundary layer scheme to reduce noise |
461 |
|
- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
462 |
|
|
463 |
|
checkpoint58n_post |
464 |
|
o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
465 |
|
local variable (not in common block). |
466 |
|
o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
467 |
|
- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
468 |
|
- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
469 |
|
to work with SingleCpuIO. |
470 |
|
o add "_d 0" to real constant of pkg/cfc subroutines ; |
471 |
|
update exp. cfc_exemple & tutorial_cfc_offline output files. |
472 |
|
o multi-threading and IO: |
473 |
|
- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
474 |
|
(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
475 |
|
- barrier before and after reading. |
476 |
|
- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
477 |
|
- avoid using MDS_WRITELOCAL for LAND pkg output. |
478 |
|
- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
479 |
|
common-block variables ; Allows multi-threading with master-thread IO. |
480 |
|
o change default MAX_NO_THREADS from 32 to 4 ; |
481 |
|
and stop cleanly when MAX_NO_THREADS is too small. |
482 |
|
o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
483 |
|
|
484 |
|
checkpoint58m_post |
485 |
|
o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
486 |
|
and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
487 |
|
o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
488 |
|
keep global_ocean.90x40x15 (for AD testing) with former secondary test |
489 |
|
(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
490 |
|
o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
491 |
|
add MITgcm_tutorials (= code + all the tutorials) |
492 |
|
o ecco, option to compute cost for total ssh (mean+anom) |
493 |
|
o consistent with addition of ptracer and ssh in pkg/profiles |
494 |
|
o profiles: adding ptracer and ssh |
495 |
|
o testreport: change multi-test output-file name |
496 |
|
(from output.txt.{name} to output.{name}.txt) |
497 |
|
o profiles: now ok for mutli-tiles case |
498 |
|
o seaice: add 4 parameters for different advection schemes for area, |
499 |
|
(effective) seaice thickness, enthalphy, and snow height. Their default |
500 |
|
is the standard parameter SEAICEadvScheme |
501 |
|
o calc_gw: |
502 |
|
- add cosFacU in zonal viscous flux (harmonic.visc.). |
503 |
|
- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
504 |
|
of tutorial_plume_on_slope. |
505 |
|
o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
506 |
|
o calc_gw: true flux-form, account for horizontal grid spacing. |
507 |
|
update rotating_tank results, but not plume_on_slope (affected at |
508 |
|
truncation level, 11 digits). |
509 |
|
|
510 |
|
checkpoint58l_post |
511 |
|
o calc_gw: |
512 |
|
- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
513 |
|
- remove side-drag for now (need to fix it); update plume_on_slope results. |
514 |
|
- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
515 |
|
o commit code to make SST/SSS weights spatially variable |
516 |
|
(based on either variable in-situ or variable initial T/S weights) |
517 |
|
o pkg/ecco: |
518 |
|
* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
519 |
|
now based on horizontally varying weights wthetaLev, wsaltLev |
520 |
|
* cost_averagesflags now returns year indices in addition to day, month |
521 |
|
* sflux balance is performed on annual basis |
522 |
|
(sflxumm, sfluxmm2, bal_sfluxmm) |
523 |
|
* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
524 |
|
including separate counting and multipliers |
525 |
|
o pkg/rbcs |
526 |
|
* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
527 |
|
|
528 |
|
checkpoint58k_post |
529 |
|
o testreport: |
530 |
|
- always build in dir. "build" (if not there, mkdir build instead of building |
531 |
|
& running in input) |
532 |
|
- run in dir run (if it exists), in build otherwise. |
533 |
|
- call prepare_run (if input/prepare_run exists) |
534 |
|
- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
535 |
|
o pkg/exf modifications to interpolation and rotation routines for more |
536 |
|
reasonable treatment of North Pole singularity: for tracers North Pole |
537 |
|
value is set to northernmost zonal-mean value, for zonal velocity it is |
538 |
|
set to zero, and for meridional velocity it is set to northernmost value. |
539 |
|
o pkg/exf/exf_check_range.F |
540 |
|
- add tile index to diagnostics and move stop statement to the very |
541 |
|
end of the routine. |
542 |
|
o pkg/diagnostics: (diagnostics_main_init.F) |
543 |
|
define title of isomorphic variables according to the current config. |
544 |
|
o pkg/thsice with pkg/seaice dynamics: |
545 |
|
- fix domain of computation (interior only, required for exf) and do exchanges |
546 |
|
- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
547 |
|
o towards a standard way of dealing with multi-threading in MONITOR |
548 |
|
and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
549 |
|
o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
550 |
|
to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
551 |
|
o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
552 |
|
o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
553 |
|
o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
554 |
|
(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
555 |
|
o tracer advection: |
556 |
|
- clean-up and simplify calc_common_factors.F |
557 |
|
- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
558 |
|
advection subroutine (but still not used within DST advection S/R) |
559 |
|
o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
560 |
|
|
561 |
|
checkpoint58j_post |
562 |
|
o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
563 |
|
from file (collects calls previously in FORWARD_STEP) |
564 |
|
o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
565 |
|
o adjoint store dir. adjusted accordingly |
566 |
|
o genmake2 |
567 |
|
replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
568 |
|
|
569 |
|
checkpoint58i_post |
570 |
|
o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
571 |
|
on wind stress (SEAICEstressFactor defaults to 1.) |
572 |
|
o Total number of Timers is finite (<=40): comment out 2 non-essential one |
573 |
|
in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
574 |
|
o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
575 |
|
on CS-grid: no longer loosing mass. |
576 |
|
o exf & curvilinear-grid: no longer modify longitude xC & xG. |
577 |
|
o pkg/ggl90: fix sloppy output and fix a bug |
578 |
|
o pkg/seaice: added SEAICEuseEVPpickup parameter |
579 |
|
- Set to false in order to start EVP solver with |
580 |
|
non-EVP pickup files when using SEAICEuseEVP |
581 |
|
- fix sign error in diffusion in seaice_calc_rhs |
582 |
|
|
583 |
|
checkpoint58h_post |
584 |
|
* Modifications for bottom topography control |
585 |
|
o replace hFacC by _hFacC at various places |
586 |
|
o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
587 |
|
o add non-self-adjoint cg2d_nsa |
588 |
|
o update autodiff support routines |
589 |
|
o re-initialise hfac after ctrl_depth_ini |
590 |
|
o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
591 |
|
* Adding verification for 5x5 box (4-layer) bottom topography control |
592 |
|
|
593 |
|
checkpoint58g_post |
594 |
|
o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
595 |
|
used for mean seasonal cycle, mean diurnal cycle); add an example |
596 |
|
in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
597 |
|
o pkg/ggl90: |
598 |
|
- add parameter (minimum surface kinetic energy) |
599 |
|
- fix bug (avoiding division by zero) |
600 |
|
o couple pkg/thsice to pkg/seaice: |
601 |
|
- modify advection in seaice to accomodate new scalar fields to be advected |
602 |
|
- only muliDimAdection scheme work with seaice/thsice |
603 |
|
- mapping of thsice-variables to seaice-variables, back and forth |
604 |
|
- does not break the verification experiments, but does not give the |
605 |
|
desired results either |
606 |
|
o pkg/seaice |
607 |
|
- make (default) second order advection a bit less confusing? |
608 |
|
|
609 |
|
checkpoint58f_post |
610 |
|
o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
611 |
|
to pkg/seaice): |
612 |
|
- new routines thsice_map_exf and thsice_get_exf provide the interface |
613 |
|
- add an additional formal parameter to thsice_solve4temp |
614 |
|
o pkg/exf: |
615 |
|
- add new fields wspeed, snowprecip (to be able to couple to thsice) |
616 |
|
- correct Stefan-Boltzmann constant |
617 |
|
- new parameter for longwave surface emittance |
618 |
|
- separate some stuff from exf_bulkformulae into new routines |
619 |
|
exf_radiation, exf_wind |
620 |
|
- add new parameters and constants: longwave emissivity for ocean, ice |
621 |
|
and snow, evaporation parameters over ice |
622 |
|
- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
623 |
|
either wind from stress or stress from wind |
624 |
|
o pkg/thSIce: |
625 |
|
- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
626 |
|
- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
627 |
|
and THSICE_CALC_THICKN |
628 |
|
- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
629 |
|
- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
630 |
|
to make debugging easier. |
631 |
|
- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
632 |
|
o pkg/bulk_force: |
633 |
|
- clean-up comments and parameters ; |
634 |
|
- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
635 |
|
o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
636 |
|
generate new output for test-experiment: aim.5l_cs.thSI |
637 |
|
o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
638 |
|
testreport accordingly |
639 |
|
|
640 |
|
checkpoint58e_post |
641 |
|
o SEAICE_CGRID adjoint done |
642 |
|
o R_STAR adjoint implemented. |
643 |
|
* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
644 |
|
* need to sort out init. of h0facc, etc. |
645 |
|
o Make pkg/profile fully independent of ecco,cost, etc. stuff |
646 |
|
to be able to use it in pure forward. |
647 |
|
|
648 |
|
checkpoint58d_post |
649 |
o upgrade simple test-experiment to tutorial example: |
o upgrade simple test-experiment to tutorial example: |
650 |
step.1: duplicate the experiment and (step.2) will remove the old copy. |
step.1: duplicate the experiment and (step.2) will remove the old copy. |
651 |
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
658 |
tutorial_global_oce_optim <- empty for now (David ?) |
tutorial_global_oce_optim <- empty for now (David ?) |
659 |
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
tutorial_global_oce_in_p <- copy of global_ocean_pressure |
660 |
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
|
|
|
661 |
o correct a sign problem in cost_scat.F |
o correct a sign problem in cost_scat.F |
662 |
o obcs and ptracers: fix boundary conditions for advections schemes |
o obcs and ptracers: fix boundary conditions for advections schemes |
663 |
with larger stencil |
with larger stencil |