4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o add another hook (S/R PDF_FINALIZE) for the Parallel Data Assimilation |
8 |
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Framework PDAF (http://pdaf.awi.de/) in the_main_loop.F |
9 |
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o pkg/autodiff: |
10 |
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- fix pkg/exf AD variable output (mainly ADJprecip), left from pkg/exf modif |
11 |
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on Jan 27, 2017. Try also to fix ADJrunoff and TLM output (but less clear). |
12 |
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o pkg/obcs: |
13 |
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- add simpler setting (single value) of OB indices for the case where |
14 |
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indices are uniform over the full section (Bruno Deremble contribution). |
15 |
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o pkg/rbcs: |
16 |
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- increase size of "relaxMaskFile" to read-in from namelist and save it |
17 |
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(+check) into new (renamed) "relaxMaskTrFile" array. |
18 |
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o model/src: |
19 |
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- option (interViscAr_pCell, interDiffKr_pCell) to account for true vertical |
20 |
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distance (including hFac) in vertical viscous flux and diffusive flux ; |
21 |
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- add option to increase vertical mixing (for both momentum and tracers) |
22 |
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near surface and/or bottom where partial cell is too thin ; |
23 |
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- for now, both additions above are within: #ifndef EXCLUDE_PCELL_MIX_CODE ; |
24 |
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|
25 |
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checkpoint66l (2017/10/24) |
26 |
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o pkg/kpp, ggl90 & ebm: |
27 |
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- read namelist without IOSTAT=errIO to force to stop if there is an error |
28 |
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in the parameter file namelist. |
29 |
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o pkg/cheapaml: major changes to relaxation coefficient setting: |
30 |
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- rename parameters cheapaml_taurelax & cheapaml_taurelaxocean (in days) |
31 |
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to cheap_tauRelax & cheap_tauRelaxOce (now in seconds); |
32 |
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- if using cheapMaskFile, set relaxation coeff to: cheapMask/tauRelax |
33 |
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(instead of 1/cheapMask over ocean and 1/tauRelax over land); |
34 |
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- with cheapMaskFile unset: set relaxation coeff according to land/ocean mask |
35 |
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(unchanged) but skip increase near domain edges for periodic domain (in X |
36 |
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or Y dir) when cheapamlX/Yperiodic=T ; also fix linear increase (over |
37 |
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Cheapaml_mask_width grid points) of coeff towards domain edges (previously |
38 |
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was increasing away from edges). Update output of experiment "cheapAML_box". |
39 |
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o pkg/cheapaml: |
40 |
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- move setting of (fixed in time) relaxation coefficient |
41 |
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from cheapaml_init_varia.F to cheapaml_init_fixed.F |
42 |
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o pkg/exf: |
43 |
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- add specific forcing field for tides to feed model new geopotential anomaly |
44 |
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forcing, for now within #ifdef EXF_ALLOW_TIDES. |
45 |
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- remove from common block unused params: exf_inscal_sst & exf_inscal_sss. |
46 |
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o model: |
47 |
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- add new 2-d forcing field for time-dependent geopotential anomaly (e.g., |
48 |
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tidal forcing), in m^2/s^2 ; add run-time param to allow to turn it off. |
49 |
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o eesupp/src: |
50 |
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- shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F |
51 |
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for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h |
52 |
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|
53 |
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checkpoint66k (2017/09/20) |
54 |
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o model/src: |
55 |
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- add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F |
56 |
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and the_model_main.F) |
57 |
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o ctrl: |
58 |
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- use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F) |
59 |
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- call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated |
60 |
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mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F, |
61 |
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ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F ) |
62 |
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o eesupp: |
63 |
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- add CPP option to activate some pieces of code for coupling to GEOS AGCM; |
64 |
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- shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM. |
65 |
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o pkg/bling: |
66 |
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- bling_production: Fix typo in calcium carbonate uptake. Also rearranging |
67 |
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and cleaning |
68 |
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o model/src: |
69 |
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- move k loop inside correction_step.F (+ update calling S/R) |
70 |
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- collect implicit pressure gradient tendencies in local 2-D array; |
71 |
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affect results (at machine truncation level) when using 3-D solver; update |
72 |
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output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW, |
73 |
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rotating_tank, short_surf_wave,tutorial_deep_convection (x2) |
74 |
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& tutorial_plume_on_slope. |
75 |
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|
76 |
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checkpoint66j (2017/08/15) |
77 |
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o pkg/ptracers: |
78 |
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- fix surface forcing under ice-shelf (useShelfIce=T). |
79 |
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o pkg/atm_phys: |
80 |
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- use hFac weighted average when applying A-grid atm-phys momentum tendency |
81 |
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to C-grid dynamics; this ensures wind-stress match mom tendency. |
82 |
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o eesupp/src: |
83 |
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- change default for opening scratch files to avoid STATUS='SCRATCH' |
84 |
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- close scratch files with STATUS='DELETE' |
85 |
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- changes affect eeset_parms.F and open_copy_data_file.F and many routines |
86 |
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that read namelists (because they close the scratch files) |
87 |
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- you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES |
88 |
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in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad) |
89 |
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o pkg/atm_phys: |
90 |
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- fix unset arguments in (unused) S/R surface_flux_0d. |
91 |
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o eesupp/src: |
92 |
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- add argument "procId" to S/R EESET_PARMS to fix scratchFile1 & 2 setting |
93 |
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(case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F): |
94 |
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called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F |
95 |
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o pkg/streamice: |
96 |
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- remove blank between _EXCH_XY_RL and "()", which my Apple Xcode |
97 |
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preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in |
98 |
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streamice_driving_stress_fd.F and streamice_advect_2dtracer.F |
99 |
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o pkg/diagnostics: |
100 |
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- new option to allow to cumulate thickness-factor (hFac) weighted field |
101 |
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(if field permitted); implemented by changing sign of "jdiag" pointer |
102 |
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(> 0: cumlulate field, < 0: cumulate hFac weighted field). |
103 |
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a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell |
104 |
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center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR') |
105 |
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b) for now, activated by setting fileFlags 3rd character to 'h'. |
106 |
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|
107 |
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checkpoint66i (2017/07/18) |
108 |
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o pkg/cheapaml: |
109 |
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- add parameter "useRelativeWind", default set to False; this change the |
110 |
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previous setting which was always using relative wind. |
111 |
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o add hooks for the Parallel Data Assimilation Framework PDAF |
112 |
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(http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F; |
113 |
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to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h |
114 |
|
o pkg/exf: |
115 |
|
- interpolation of vector fields (exf_interp_uv.F): fix bug in calculation |
116 |
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of South-Pole mean value. |
117 |
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- interpolation near the poles, case where second additional row is at the |
118 |
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pole (or beyond the pole and moved to the pole): change first addition row |
119 |
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value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole) |
120 |
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row (instead of just a copy of it). |
121 |
|
o pkg/seaice: |
122 |
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- prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0 |
123 |
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- add the option to compute no-slip du/dy, dv/dx (i.e. |
124 |
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the offdiagonal strain rate e12) by a second order approximation |
125 |
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on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because |
126 |
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it is too messy to implement for the implicit LSR matrix. |
127 |
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SEAICE_2ndOrderBC = .FALSE. by default |
128 |
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|
129 |
|
checkpoint66h (2017/06/02) |
130 |
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o pkg/seaice: |
131 |
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- add new routines to compute stress tensor components and stress tensor |
132 |
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divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs |
133 |
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- change names of diagnostics SIsigI/II (commonly used for invariants) |
134 |
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to SIsig1/sig2 (more common for principal components) to avoid confusion |
135 |
|
o pkf/exf: |
136 |
|
- add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant); |
137 |
|
similarly, stop if rotateStressOnAgrid with constant wind-stress. |
138 |
|
o pkg/seaice: |
139 |
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- remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of |
140 |
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EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent. |
141 |
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- add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice |
142 |
|
fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy). |
143 |
|
o pkg/diagnostics: |
144 |
|
- small piece of code to rename (old) diagnostics, when namelist is processed. |
145 |
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o model/src: |
146 |
|
- new run-time param (useMin4hFacEdges) to select method for setting hFacW,S: |
147 |
|
originally, set as minimum of adjacent hFacC factor ; now (new default) |
148 |
|
computed from rSurfW,S and rLowW,S by applying same rules as for hFacC. |
149 |
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Only matters when useShelfIce=T with particular ice-shelf cavity geometry. |
150 |
|
o pkg/seaice: |
151 |
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- add momemtum advection, off by default, still in test phase |
152 |
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most of the momentum advection code is adapted and reused from mom_vecinv |
153 |
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o pkg/mom_vecinv: |
154 |
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- pass these runtime flags: |
155 |
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selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv |
156 |
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as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4, |
157 |
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so that these routines can also be used in pkg/seaice. |
158 |
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|
159 |
|
checkpoint66g (2017/04/24) |
160 |
|
o model/src: |
161 |
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- more robust ordering of column thickness integral (=Sum_k(drF*hFac) ) |
162 |
|
to get same expression (regarding machine truncation) in different places |
163 |
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in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should). |
164 |
|
Update forward output of experiments: global_ocean.cs32x15 (all 5 except |
165 |
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viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope. |
166 |
|
o pkg/shelfice: |
167 |
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- ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F |
168 |
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to shelfice_init_fixed.F |
169 |
|
- change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from |
170 |
|
ini_masks_etc.F for now) to update ocean upper boundary position according |
171 |
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to ice-shelf topography (instead of directly updating hFacC). |
172 |
|
o model/src: |
173 |
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- move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of |
174 |
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packages_init_fixed.F to allow other pkgs to set mask and weight fields. |
175 |
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|
176 |
|
checkpoint66f (2017/04/06) |
177 |
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o model/src: |
178 |
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- add specific run-time param to select level of printed plot-field-maps, |
179 |
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set by default to debugLevel. Remove internal param "printDomain". |
180 |
|
o pkg/seaice: |
181 |
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- add flag to add snow mass to seaiceMassC/U/V, the default is |
182 |
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SEAICEaddSnowMass=.FALSE., not to change previous results |
183 |
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o pkg/bling |
184 |
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- Bug fix in bling_production regarding unit conversion for diagnostics |
185 |
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being put in the wrong place |
186 |
|
o model/src: |
187 |
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- add back recomputation of rSurfW & S to ensure consistent column thickness |
188 |
|
(needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only |
189 |
|
when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F |
190 |
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revision 1.51) but was removed accidentally on 2014/02/08 (v1.53). |
191 |
|
o pkg/autodiff: |
192 |
|
- clean-up "checkpoint.flow" |
193 |
|
o pkg/rw (Contribution from Jody Klymak): |
194 |
|
option to set mds file suffix as function of time in simulation: |
195 |
|
*) new input parameter "rwSuffixType" (read from PARM03 namelist) |
196 |
|
to select file suffix format; by default (=0), use iteration number; |
197 |
|
*) add simple routine to return file suffix according to rwSuffixType; |
198 |
|
*) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice), |
199 |
|
use new S/R to get file suffix, except for debug output file (diagFreq) |
200 |
|
and pkgs offline & rbcs input files. |
201 |
|
o pkg/rw: |
202 |
|
- uniform processing of "I10" suffix across writing fld routines; used to |
203 |
|
simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F |
204 |
|
(similar to cg3d.F, cg3d_ex0.F) |
205 |
|
o pkg/mom_vecinv: |
206 |
|
- highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted |
207 |
|
vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp). |
208 |
|
o pkg/bling: |
209 |
|
- Many small changes intended to clean the code. |
210 |
|
Unnecessary ADJOINT_SAFEs removed ; |
211 |
|
removed BLING_COST.h BLING_CTRL.h bling_cost.F ; |
212 |
|
diagnostics added. |
213 |
|
|
214 |
|
checkpoint66e (2017/03/14) |
215 |
|
o pkg/exf: |
216 |
|
- interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size |
217 |
|
definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h; |
218 |
|
use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to |
219 |
|
avoid any dynamic allocation ; |
220 |
|
- S/R EXF_CHECK: add new check & stop when file-name is defined but not |
221 |
|
read-in ; add warning when file is read-in but not used within pkg/exf ; |
222 |
|
+ check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC). |
223 |
|
- update exf_summary.F (print {FLD}RepCycle). |
224 |
|
o verification/global_with_exf: |
225 |
|
- switch on exf interpolation in AD test (just like the forward test) |
226 |
|
o pkg/mom_vecinv: |
227 |
|
- add storage directives to avoid recomputations within mom_vecinv.F |
228 |
|
which were generating seg. fault with gfortran -devel |
229 |
|
o pkg/ctrl, pkg/smooth: |
230 |
|
- initialize array halos which were generating seg. fault with |
231 |
|
gfortran -devel in adjoint mode |
232 |
|
o pkg/exf: |
233 |
|
- for each input field, enable to specify a field specific repeat-cycle |
234 |
|
({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod". |
235 |
|
o verification/lab_sea: |
236 |
|
- update AD results of primary test and noseaicedyn test after switching |
237 |
|
to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient |
238 |
|
check stays about the same. |
239 |
|
o pkg/exf: |
240 |
|
- fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T. |
241 |
|
- exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat |
242 |
|
o pkg/bling, USE_EXFCO2 code: |
243 |
|
- add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default); |
244 |
|
- update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD). |
245 |
|
o pkg/exf: |
246 |
|
- rename S/R EXF_INIT to EXF_INIT_VARIA ; |
247 |
|
- add arguments: fldName (for debug msg) and fldRepeatCycle (set to |
248 |
|
repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD) |
249 |
|
and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ; |
250 |
|
- add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed |
251 |
|
EXF_INIT_FLD) and update calls in exf_init_varia.F |
252 |
|
- For now, for backward compatibility, keep a simplified version of S/Rs |
253 |
|
EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F |
254 |
|
- add and pass new arguments: fldName (for debug msg) and fldRepeatCycle |
255 |
|
to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F |
256 |
|
o tools/genmake2: |
257 |
|
- replace "bc -l" (only used once) by "expr" (already used). |
258 |
|
o verification/global_ocean.cs32x15: |
259 |
|
- turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn". |
260 |
|
Note: exf setting (data.exf) can be compared to other exf secondary exp |
261 |
|
"seaice" (kept with useCAL=T) which has same time dependent forcing. |
262 |
|
|
263 |
|
checkpoint66d (2017/02/13) |
264 |
|
o pkg/exf: |
265 |
|
- remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning |
266 |
|
early on (in packages_boot.F) to stress this change in pkg setting. |
267 |
|
- In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg |
268 |
|
o model/src: |
269 |
|
- move call to ecco_phys to end of time step; this may induce minor |
270 |
|
cost function changes by shifting time averages by one time step |
271 |
|
for some variables; this revision resulted in changed adjoint results |
272 |
|
in MITgcm_contrib/verification_other/global_oce_cs32 |
273 |
|
o pkg/exf: |
274 |
|
- Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ; |
275 |
|
this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields, |
276 |
|
e.g. precip, are not available. |
277 |
|
o pkg/flt: |
278 |
|
- flt_init_varia.F: use pickupSuff if specified |
279 |
|
- add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first, |
280 |
|
intermediate, step towards completing pkg/exch2 support within pkg/flt; |
281 |
|
ifdef DEVEL_FLT_EXCH2 then: |
282 |
|
- flt_init_fixed.F: comment out stop |
283 |
|
- flt_exch2.F: conserve ipart, jpart (grid coordinates) |
284 |
|
- exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates) |
285 |
|
- flt_mapping.F: attempt to fix longitude diagnostic near date-line |
286 |
|
- flt_init_varia.F: hack initialization (for testing purposes w. LLC90) |
287 |
|
o tools/genmake2 & pkg/pkg_depend: |
288 |
|
- define new type of pkg dependency rule ("=pkg_x"), less strict than |
289 |
|
the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled |
290 |
|
(-pkg_x in packages.conf). |
291 |
|
- change pkg/exf dependency rule from "exf +cal" to "exf =cal"; |
292 |
|
- add "+cal" to dependency list of pkg/ecco (needed to compile). |
293 |
|
- simplify FWD experiment "offline_exf_seaice" by removing pkg/cal. |
294 |
|
o utils/matlab: |
295 |
|
- adding ocean_basin routines for defining basin masks. |
296 |
|
o pkg/exf: |
297 |
|
- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
298 |
|
arguments, allowing to check (and stop) if parameter setting of |
299 |
|
{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
300 |
|
useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
301 |
|
for backward compatibility. |
302 |
|
- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
303 |
|
exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
304 |
|
o pkg/bling (USE_EXFCO2 code): |
305 |
|
- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
306 |
|
by adding a call to S/R EXF_GETFFIELD_START. |
307 |
|
o pkg/exf: |
308 |
|
- allows to compile without pkg/cal (but disabled by current dependency |
309 |
|
rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
310 |
|
run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
311 |
|
of {FLD}startdate1 & date2 ; consistency check not yet coded. |
312 |
|
o verification/global_ocean.cs32x15: |
313 |
|
- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
314 |
|
corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
315 |
|
o pkg/exf: |
316 |
|
- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
317 |
|
calculations); change FWD experiment global_ocean.cs32x15 |
318 |
|
(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
319 |
|
o pkg/exf: |
320 |
|
- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
321 |
|
{FIELD}startdate to {FIELD}StartTime |
322 |
|
Note: new name also fit better the content, i.e, a start time in second. |
323 |
|
o eesupp/src: |
324 |
|
- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
325 |
|
o pkg/exf: |
326 |
|
- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
327 |
|
to allow to read-in Sensible & Latent Heat flux ; |
328 |
|
- simplify pkg/exf main options: |
329 |
|
1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
330 |
|
exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
331 |
|
compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
332 |
|
2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
333 |
|
ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
334 |
|
3) improve options documentation in EXF_OPTIONS.h. |
335 |
|
o pkg/ecco: |
336 |
|
- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
337 |
|
ecco_summary.F: add passive tracer cost functions to gencost; |
338 |
|
m_ptracer and m_boxmean_ptracer |
339 |
|
o pkg/ctrl: |
340 |
|
- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
341 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
342 |
|
of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
343 |
|
xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
344 |
|
o model/src: |
345 |
|
- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
346 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
347 |
|
o pkg/exf: |
348 |
|
- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
349 |
|
xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
350 |
|
|
351 |
|
checkpoint66c (2017/01/19) |
352 |
|
o verification: |
353 |
|
- add new option "-src" to testreport to only produce source code (*.f), |
354 |
|
including taf output src code (if using '-adm'/'-tlm' option). |
355 |
|
o pkg/exf: |
356 |
|
- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
357 |
|
o pkg/diagnostics: |
358 |
|
- add run-time variable diagMdsDir to specify a subdirectory for |
359 |
|
diagnostic output when mds is being used and mdsioLocalDir is not. |
360 |
|
o pkg/mnc: |
361 |
|
- mnc_utils.F: edit stop message |
362 |
|
o pkg/autodiff: |
363 |
|
- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
364 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
365 |
|
o pkg/profiles: |
366 |
|
- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
367 |
|
profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
368 |
|
- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
369 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
370 |
|
o pkg/smooth: |
371 |
|
- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
372 |
|
- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
373 |
|
- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
374 |
|
o pkg/exf: |
375 |
|
- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
376 |
|
issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
377 |
|
generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
378 |
|
- summary: skip detailed field report if not used (empty file-name). |
379 |
|
o tools/xmakedepend: |
380 |
|
- In case line editor "ed" is missing, switch to "sed" command to clean-up |
381 |
|
Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
382 |
|
o pkg/exf: |
383 |
|
- change definition of "hflux" input file to always include Short-Wave; |
384 |
|
this is now consistent with hflux computation (if using bulk-formulae) |
385 |
|
and hflux diagnostic & documentation (in EXF_FIELDS.h). |
386 |
|
|
387 |
|
checkpoint66b (2016/12/01) |
388 |
|
o model & momentum pkgs: |
389 |
|
- implement fully implicit bottom friction combined with implicit surf. |
390 |
|
pressure, for now, only in hydrostic formulation: |
391 |
|
+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
392 |
|
and run with selectImplicitDrag=2 ; |
393 |
|
+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
394 |
|
- partial implicit time-stepping (bot. friction + vert. visc first, then |
395 |
|
surf. press) corresponding to selectImplicitDrag=1 should be applicable |
396 |
|
to NH formulation but not available until we solve for surf. pressure |
397 |
|
increment (instead of full etaN). |
398 |
|
- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
399 |
|
with implicit vertical viscosity. |
400 |
|
o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
401 |
|
- this is a first version that includes many regularisations that may |
402 |
|
not all be necessary, to be sorted out, |
403 |
|
- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
404 |
|
- change one verification experiment in seaice_itd to use and test new code |
405 |
|
- seaice_growth: catch a case where the argument of log can be zero |
406 |
|
or smaller (important for code stability) |
407 |
|
o model/src: |
408 |
|
- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
409 |
|
& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
410 |
|
similar A.X'=Y' system (with same matrix A) in subsequent calls; |
411 |
|
switch based on errCode (In/Out) argument value; in calling routines, |
412 |
|
initialise errCode before first call. |
413 |
|
|
414 |
|
checkpoint66a (2016/10/18) |
415 |
|
o pkg/bling: |
416 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
417 |
|
Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
418 |
|
o model/src & pkg/ptracers: |
419 |
|
- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
420 |
|
GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
421 |
|
implicitDiffusion (respectively) are used (even without momImplVertAdv |
422 |
|
or temp,salt,PTRACERS_ImplVertAdv). |
423 |
|
o model/src & generic_advdiff: |
424 |
|
- add parenthesis in main diagonal calculation of implicit vertical |
425 |
|
diffusion matrix (impldiff.F & gad_implicit_r.F). |
426 |
|
This affects results at machine truncation level; update output of many |
427 |
|
verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
428 |
|
o pkg/mom_commom & generic_advdiff: |
429 |
|
- add deep atmosphere and anelastic scaling factor in implicit vertical |
430 |
|
advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
431 |
|
o model/src: |
432 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
433 |
|
& solve_pentadiagonal.F |
434 |
|
|
435 |
|
checkpoint65z (2016/09/28) |
436 |
|
o pkg/seaice: fix multithreading for seaice_fgmres.F |
437 |
|
- remove unecessary variables from common blocks |
438 |
|
- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
439 |
|
basis, that are stored in commom blocks (including integer variable i1) |
440 |
|
- clean up code a little by removing commented lines that refer to |
441 |
|
original code |
442 |
|
- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
443 |
|
o MITgcm manual: |
444 |
|
- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
445 |
|
preliminary documentation for generic controls (8.3; ctrl.tex), |
446 |
|
a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
447 |
|
ecco_costfunction.tex |
448 |
|
o pkg/ecco: |
449 |
|
- update and cleanup list of CCP options |
450 |
|
- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
451 |
|
is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
452 |
|
- add checks that retired run-time options are not used, and in relation |
453 |
|
to gencost_mask and gencost_errfile |
454 |
|
- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
455 |
|
gencost_nrecperiod |
456 |
|
- fix m_eta computation for virtual salt flux case |
457 |
|
- add m_horflux_vol case (selected via gencost_barfile) that computes |
458 |
|
transports via cost_gencost_boxmean (gencost_flag=-3) |
459 |
|
- use gencost_flag more systematically (i.e., avoid using gencost_name) |
460 |
|
for code switches (aside from physical variable selection) |
461 |
|
o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
462 |
|
attempt appears to be a bit of a hack and my need some repair down the road |
463 |
|
o pkg/exf: |
464 |
|
- interpolation near South Pole: fix criteria on input field latitude. |
465 |
|
o pkg/icefront & pkg/exf: |
466 |
|
- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
467 |
|
from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
468 |
|
o pkg/exf: |
469 |
|
- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
470 |
|
"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
471 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
472 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
473 |
|
Change output file content by writing interpolated field before applying |
474 |
|
land-sea mask (helpful for debug). |
475 |
|
- 2 compon. vector interpolation with rotation: apply scaling factor on |
476 |
|
each compon. (Eastward and Northward) just before rotation. |
477 |
|
o pkg/bling: |
478 |
|
- Cleaned package. Removed not needed code and comments. |
479 |
|
- adjoint example now works |
480 |
|
(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
481 |
|
o pkg/ptracers: |
482 |
|
- add Bruno Deremble's code to complete the linear surface correction |
483 |
|
for tracer conservation; |
484 |
|
- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
485 |
|
|
486 |
|
checkpoint65y (2016/07/29) |
487 |
|
o pkg/debug (stats): |
488 |
|
- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
489 |
|
proc/thread mapping); |
490 |
|
- fix Min & Max for case where 1 thread has only empty tiles; |
491 |
|
- use RL variable to count number of wet grid points (with big domain, |
492 |
|
can be too large to fit into integer*4). |
493 |
|
o pkg/monitor: |
494 |
|
- use RL variable to count number of wet grid points (but used only for del2) |
495 |
|
- add new routine to compute Advective CFL within tracer time-stepping with |
496 |
|
writing delayed until next monitor output. |
497 |
|
o pkg/obcs: |
498 |
|
- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
499 |
|
o pkg/cal: |
500 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
501 |
|
eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
502 |
|
o pkg/dic & seaice: |
503 |
|
- fix compilation of ocean component for coupled atm+ocn model with |
504 |
|
seaice dynamics & dic. |
505 |
|
|
506 |
|
checkpoint65x (2016/06/11) |
507 |
|
o add a license text file in main MITgcm tree. |
508 |
|
o added pkg/bling: |
509 |
|
- intermediate complexity biogeochemical model |
510 |
|
- see bling_description.txt for details |
511 |
|
- verification experiment is global_oce_biogeo_bling (for now, in |
512 |
|
Contrib/verification_other/); tested daily on baudelaire with gfortran. |
513 |
|
- add entry point in pkg/gchem for new pkg "bling". |
514 |
|
o pkg/seaice: fix tensile stength computation |
515 |
|
- replace global field tensileStrength by tensileStrFac |
516 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
517 |
|
- fortunately that does not affect any verification results |
518 |
|
|
519 |
|
checkpoint65w (2016/05/12) |
520 |
|
o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
521 |
|
with ECCO_CTRL_DEPRECATED defined |
522 |
|
o verification/global_ocean.cs32x15: |
523 |
|
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
524 |
|
with "selectNHfreeSurf=1". |
525 |
|
o model/src (non-hydrostatic free-surface): |
526 |
|
- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
527 |
|
was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
528 |
|
- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
529 |
|
for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
530 |
|
and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
531 |
|
This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
532 |
|
- Update output (changes at machine truncation level) of verification exp: |
533 |
|
exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
534 |
|
short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
535 |
|
o pkg/seaice: ITD code |
536 |
|
- fix picking up from a single category model by initialising |
537 |
|
heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
538 |
|
- split a long warning message in seaice_check_pickup.F into two lines, |
539 |
|
because NEC SX-ACE cannot deal with the long line. |
540 |
|
o model/src: |
541 |
|
- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
542 |
|
o pkg/seaice: |
543 |
|
- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
544 |
|
o pkg/seaice: |
545 |
|
- add basal stress as parameterisation for grounding ice |
546 |
|
following Lemieux et al. (2015) |
547 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
548 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
549 |
|
- The adjoint complains with extra recomputations so there is also a |
550 |
|
new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
551 |
|
order to postpone the problem |
552 |
|
- compile the new code in lab_sea |
553 |
|
o verification/halfpipe_streamice: |
554 |
|
- update both TAF and OpenAD adm output (machine truncation differences) |
555 |
|
|
556 |
|
checkpoint65v (2016/04/08) |
557 |
|
o verification/advect_xz: |
558 |
|
- increase overlap size from 3 to 4 and add new secondary test for PQM |
559 |
|
advection scheme (with mono & wino limiter). |
560 |
|
- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
561 |
|
o model/src: |
562 |
|
- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
563 |
|
added phi0Ref) to set vertical axis origin and phiRef origin; |
564 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
565 |
|
According to coordinate and fluid type: |
566 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
567 |
|
ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
568 |
|
OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
569 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
570 |
|
- remove Ro_SeaLevel from ATM experiment parameter files; |
571 |
|
- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
572 |
|
complement; update output.txt (changes at machine truncation level). |
573 |
|
o pkg/seaice/seaice_evp.F |
574 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
575 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
576 |
|
verification experiment lab_sea.hb87 -> updated |
577 |
|
|
578 |
|
checkpoint65u (2016/03/14) |
579 |
|
o pkg/generic_advdiff: |
580 |
|
- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
581 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
582 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
583 |
|
testing and not for actual use. |
584 |
|
o model/src: |
585 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
586 |
|
origin r = rF(1); |
587 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
588 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
589 |
|
more accurate pressure vertical profile; options not linked to EOS type |
590 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
591 |
|
- start to implement variable gravity (along vertical): for now, only with |
592 |
|
z-coords (not even z*). |
593 |
|
- add Ideal Gas equation of state for height coordinate. |
594 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
595 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
596 |
|
o pkg/exf: |
597 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
598 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
599 |
|
to velocity point) for each field that gets loaded from file. This option |
600 |
|
identically mimics the input file organization (e.g. record numbers in year |
601 |
|
by year input files) besides the change in horizontal grid. |
602 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
603 |
|
can be provided on the A-grid in zonal/meridional direction and |
604 |
|
rotated on the fly. This only applies to the case when the exf |
605 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
606 |
|
o model/src: |
607 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
608 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
609 |
|
inactive, src code yet to come) |
610 |
|
|
611 |
|
checkpoint65t (2016/02/10) |
612 |
|
o pkg/atm_phys: |
613 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
614 |
|
o model/src: |
615 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
616 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
617 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
618 |
|
o tools: |
619 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
620 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
621 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
622 |
|
o pkg/seaice: |
623 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
624 |
|
has an effect |
625 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
626 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
627 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
628 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
629 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
630 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
631 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
632 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
633 |
|
use with SEAICEuseKrylov |
634 |
|
o pkg/seaice/seaice_lsr.F |
635 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
636 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
637 |
|
an effect. |
638 |
|
o pkg/seaice: add two new parameters |
639 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
640 |
|
parameter is not in any namelist) |
641 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
642 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
643 |
|
solver |
644 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
645 |
|
affects some experiments at truncation level: |
646 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
647 |
|
- global_ocean.cs32x15.seaice (11 digits), |
648 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
649 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
650 |
|
o pkg/salt_plume & pkg/thsice: |
651 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
652 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
653 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
654 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
655 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
656 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
657 |
|
o pkg/dic: |
658 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
659 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
660 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
661 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
662 |
|
(previously done in ocn_apply_import.F). |
663 |
|
o tools/adjoint_options: |
664 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
665 |
|
has been changed on Jan 14, 2016. |
666 |
|
o pkg/ggl90: |
667 |
|
- add alternative discretisation of vertical shear (off by default), to |
668 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
669 |
|
vertical shear of mean flow (@ grid-cell center). |
670 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
671 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
672 |
|
o pkg/atm_compon_interf: |
673 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
674 |
|
pass last value, stored directly before export to CPL ; |
675 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
676 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
677 |
|
|
678 |
|
checkpoint65s (2016/01/13) |
679 |
|
o eesupp & genmake2: |
680 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
681 |
|
ETIME and consistent output; use the appropriate version in timers.F |
682 |
|
o model/src: |
683 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
684 |
|
integr_continuity; turned off by default. |
685 |
|
o pkg/dic: |
686 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
687 |
|
o tools/tst_2+2: |
688 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
689 |
|
to fail for no good reason. |
690 |
|
o eesupp & genmake2: |
691 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
692 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
693 |
|
o coupler pkgs: |
694 |
|
Finish implementation of optionally-exchanged variable switches (started on |
695 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
696 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
697 |
|
advection in OCN component; this requires sequential coupling. |
698 |
|
coupler (pkg/atm_ocn_coupler): |
699 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
700 |
|
routines (useful for debug). |
701 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
702 |
|
flux, DIC fields) if corresponding switch is ON. |
703 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
704 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
705 |
|
components (pkg/atm_ & ocn_compon_interf): |
706 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
707 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
708 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
709 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
710 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
711 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
712 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
713 |
|
- hold in common block coupler optionally-exchanged variable switch |
714 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
715 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
716 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
717 |
|
to contain new additional exchanged fields). |
718 |
|
o pkg/dic: |
719 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
720 |
|
o pkg/thsice: |
721 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
722 |
|
and writing of thsice pickup files. |
723 |
|
o pkg/atm_compon_interf: |
724 |
|
- move all field individual export-call out of cpl_export_import_data.F |
725 |
|
into new S/R ATM_EXPORT_FIELDS |
726 |
|
o pkg/atm_compon_interf: |
727 |
|
- store state variables (for now, only thSIce fields) just before beeing |
728 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
729 |
|
atm_store_my_data.F like all exported fluxes. |
730 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
731 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
732 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
733 |
|
o pkg/dic: |
734 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
735 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
736 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
737 |
|
value can be from domain [0,1] to average between the two methods |
738 |
|
o pkg/atm_phys: |
739 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
740 |
|
hold fixed in time). |
741 |
|
|
742 |
|
checkpoint65r (2015/12/21) |
743 |
|
o pkg/seaice: |
744 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
745 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
746 |
|
o pkg/seaice: |
747 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
748 |
|
when SEAICEscaleSurfStress=.TRUE., |
749 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
750 |
|
o pkg/atm_phys: |
751 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
752 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
753 |
|
for individual contribution (convection, LSC cond, radiation) |
754 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
755 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
756 |
|
o pkg/ggl90: |
757 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
758 |
|
avoid instability problems in the explicit horizontal diffusion term for |
759 |
|
long time steps or high resolution |
760 |
|
o pkg/diagnostics: |
761 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
762 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
763 |
|
o testreport: |
764 |
|
- remove "-v" (verbose option) in default mpirun command. |
765 |
|
o pkg/seaice/seaice_growth: |
766 |
|
- catch potential division by zero in ITD code, does not change |
767 |
|
verification results |
768 |
|
o pkg/ecco: |
769 |
|
- retire old codes to the Attic. The calls to retired functions are |
770 |
|
left in a commented form in case they ever need to be re-activated. |
771 |
|
- ecco_check.F: issue warning if any old CPP option is |
772 |
|
defined that corresponds to retired codes -- then stop. |
773 |
|
o pkg/atm_compon_interf: |
774 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
775 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
776 |
|
time-step, similar to what is done for seaIceMass. |
777 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
778 |
|
o eesupp & genmake2: |
779 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
780 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
781 |
|
o pkg/seaice/seaice_evp: |
782 |
|
- refine residual computation |
783 |
|
|
784 |
|
checkpoint65q (2015/11/18) |
785 |
|
o pkg/seaice/seaice_evp: |
786 |
|
- fix residual computations so that they no longer affect the actual |
787 |
|
simulation code |
788 |
|
- fix seaice_readparams to be able to actually set new parameters |
789 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
790 |
|
o model/src: |
791 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
792 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
793 |
|
a) replaced by DFLOAT (if not seen by TAF); |
794 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
795 |
|
o pkg/aim_v23: |
796 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
797 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
798 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
799 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
800 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
801 |
|
add corresponding call in DO_OCEANIC_PHYS. |
802 |
|
o coupler pkgs: |
803 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
804 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
805 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
806 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
807 |
|
compononent param default can be set accordingly). |
808 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
809 |
|
but rather applies to a group a fields (going both ways like for DIC) |
810 |
|
and corresponds to an option of coupling config. |
811 |
|
coupler (pkg/atm_ocn_coupler): |
812 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
813 |
|
and read namelist directly (without eessup S/R calls) instead of |
814 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
815 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
816 |
|
cleanly in CPL_CHECK_CPLCONFIG |
817 |
|
- add new coupling-exchange selectors (some not yet active) including |
818 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
819 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
820 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
821 |
|
component ; called directly from coupler.F, after comp. registrations; |
822 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
823 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
824 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
825 |
|
components (pkg/atm_ & ocn_compon_interf): |
826 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
827 |
|
CPP header file in all pkg source files. |
828 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
829 |
|
ATM/OCN_CHECK_CPLCONFIG; |
830 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
831 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
832 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
833 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
834 |
|
before PACKAGES_READPARMS; |
835 |
|
verification/cpl_aim+ocn/: |
836 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
837 |
|
"data.cpl" for coupler (in input_cpl). |
838 |
|
o eesupp/inc: |
839 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
840 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
841 |
|
to always cumulate tile local-sum in the same order (still uses |
842 |
|
MPI_Allreduce like standard code). |
843 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
844 |
|
that are now identical to standard version (in eesupp/inc). |
845 |
|
o pkg/shelfice: |
846 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
847 |
|
heat and salt transfer coefficients |
848 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
849 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
850 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
851 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
852 |
|
o pkg/atm_ocn_coupler: |
853 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
854 |
|
o pkg/rbcs: |
855 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
856 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
857 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
858 |
|
|
859 |
|
checkpoint65p (2015/10/23) |
860 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
861 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
862 |
|
solution, but at least there are no more recomputation warnings left |
863 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
864 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
865 |
|
o tools/adjoint_options/adjoint_diva: |
866 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
867 |
|
o pkg/streamice: |
868 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
869 |
|
o pkg/exf: |
870 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
871 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
872 |
|
o pkg/seaice: |
873 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
874 |
|
5 additionals 2D fields and 6 new store directives |
875 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
876 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
877 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
878 |
|
or SEAICEaEVPcoeff |
879 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
880 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
881 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
882 |
|
- this is an intermediate state of a truely converging EVP that has |
883 |
|
the potential of outperforming implicit VP methods, I do not recommend |
884 |
|
using it yet. |
885 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
886 |
|
and all parameters are hardwired |
887 |
|
- for convergence it still requires very smooth regularisations, that means, |
888 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
889 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
890 |
|
specific averaging appears to be required, still subject to tuning |
891 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
892 |
|
- add code to compute and print residuals of iteration, compile with |
893 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
894 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
895 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
896 |
|
|
897 |
|
checkpoint65o (2015/09/14) |
898 |
|
o pkg/mom_vecinv & mom_common: |
899 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
900 |
|
called from there. |
901 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
902 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
903 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
904 |
|
and Koenig-Beatty+Holland (2012) |
905 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
906 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
907 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
908 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
909 |
|
(to be changed and played with, for now exponential) |
910 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
911 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
912 |
|
by AREA according to Connelly et al. (2004), JPO. |
913 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
914 |
|
the only non-zero term in the denominator when there is no ice (which |
915 |
|
prevented running the model with zero ice-ocean drag). If |
916 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
917 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
918 |
|
consequence is that for open water, the momentum equation reduce |
919 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
920 |
|
they happen to be zero, often leading to a non-zero solution over |
921 |
|
open water. |
922 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
923 |
|
efficient EVP method. |
924 |
|
- introduce area-weighted averages for e12 (analogously to |
925 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
926 |
|
remain, but also changing the order of terms in the previous average |
927 |
|
changed the results as much) -> update experiment |
928 |
|
- add SEAICE_DELTA_SMOOTHREG code |
929 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
930 |
|
TEM-code |
931 |
|
- adjust loop bounds so that only required fields are computed |
932 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
933 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
934 |
|
results again), but will replace old code eventually |
935 |
|
o eesupp/src: |
936 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
937 |
|
to always cumulate tile local-sum in the same order |
938 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
939 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
940 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
941 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
942 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
943 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
944 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
945 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
946 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
947 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
948 |
|
|
949 |
|
checkpoint65n (2015/07/29) |
950 |
|
o pkg/thsice: |
951 |
|
- add a warning when used with pkg/aim but without updating SST |
952 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
953 |
|
o pkg/offline: |
954 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
955 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
956 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
957 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
958 |
|
These changes allow: |
959 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
960 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
961 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
962 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
963 |
|
b) no needs to switch on staggerTimeStep anymore; |
964 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
965 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
966 |
|
o pkg/offline: |
967 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
968 |
|
can easily recover previous offset-iter effect by setting offset-time |
969 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
970 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
971 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
972 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
973 |
|
o OpenAD |
974 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
975 |
|
Config. with ggl90 currently diverges after 64 time steps |
976 |
|
so will need more work to become more stable |
977 |
|
- Adding preliminary kpp test to OpenAD verification. |
978 |
|
required small tweakes in kpp_routines.F |
979 |
|
- Merge and update from Krishna Narayanan's contrib area: |
980 |
|
* Add one variable for preliminary OpenAD DIVA |
981 |
|
* Add replacement time-stepping for OpenAD DIVA |
982 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
983 |
|
* required modifs for OAD_support |
984 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
985 |
|
o pkg/seaice: |
986 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
987 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
988 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
989 |
|
(no effect on EVP) |
990 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
991 |
|
o pkg/seaice: |
992 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
993 |
|
for regularizing Delta (and nothing else, like the parameter |
994 |
|
which is also used for all sorts of things SEAICE_EPS). |
995 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
996 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
997 |
|
the wrong key by inialising it before use -> fixes a recomputation |
998 |
|
problem but does not fix the gradient |
999 |
|
o pkg/layers: |
1000 |
|
- move resetting of flux arrays to outside the iLa loop |
1001 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
1002 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
1003 |
|
o pkg/layers: |
1004 |
|
- remove from common block 3D layers fields (used to diagnose transport |
1005 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
1006 |
|
o pkg/seaice: |
1007 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
1008 |
|
in lab_sea forward experiment (changes results -> updated) |
1009 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
1010 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
1011 |
|
computations; for SEAICE_VECTORIZE_LSR |
1012 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
1013 |
|
sweep to the outside, |
1014 |
|
- remove store directives and add "CADJ loop sequential" directives |
1015 |
|
in analogy to model/src/solve_tridiagonal.F |
1016 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
1017 |
|
boundaries to yield more readable code. This has also the charming side |
1018 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
1019 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
1020 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
1021 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
1022 |
|
an additional option) |
1023 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
1024 |
|
but the adjoint gradients (which are affected by this change) still explode. |
1025 |
|
o coupler (atm & ocn _compon_interf): |
1026 |
|
- avoid using Exch2 IO mapping if not suitable. |
1027 |
|
|
1028 |
|
checkpoint65m (2015/06/15) |
1029 |
|
o pkg/layers: |
1030 |
|
- clean-up old parameters setting (from Sep 2012): |
1031 |
|
+ remove old parameters setting from common block (declared locally); |
1032 |
|
+ stop if any old parameter is mixed with new parameters; |
1033 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
1034 |
|
- check that layers_bounds for Pot.Density are in the right range; |
1035 |
|
this is supposed to catch un-updated setting after recently shifting |
1036 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
1037 |
|
o pkg/layers: |
1038 |
|
- Added missing call to layers_fill for keeping track of tottend in |
1039 |
|
pkg/diagnostics/diagnostics_fill_state.F |
1040 |
|
o pkg/layers: |
1041 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
1042 |
|
of diapycnal fluxes |
1043 |
|
o pkg/layers: |
1044 |
|
- reverted changes to interpolation to previous treatment; there |
1045 |
|
was never actually a problem |
1046 |
|
o pkg/layers: |
1047 |
|
- fix interpolation of layers tracers in the presence of partial cells |
1048 |
|
- add lots of new functionality to compute water mass transformation |
1049 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
1050 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
1051 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
1052 |
|
for layers_thermodynamics calculations |
1053 |
|
o pkg/ptracers: |
1054 |
|
- add capability of stepping a passive tracer forward without advection |
1055 |
|
by setting PTRACERS_advScheme to 0. |
1056 |
|
o pkg/diagnostics: |
1057 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
1058 |
|
o pkg/layers: |
1059 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
1060 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
1061 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
1062 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
1063 |
|
o pkg/layers: |
1064 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
1065 |
|
- fix calculation of layer non-weighted velocity and layer probability |
1066 |
|
- add diagnostics for pot.density used for layer averaging |
1067 |
|
o pkg/seaice: |
1068 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
1069 |
|
positiveness, modify a few comments and improve variable names, |
1070 |
|
- the changed computation of deltaC affects most seaice-related |
1071 |
|
experiments at the truncation level. |
1072 |
|
seaice_itd.thermo is affected by far the most, with |
1073 |
|
only 7 digits of agreement remaining; update experiments. |
1074 |
|
|
1075 |
|
checkpoint65l (2015/05/04) |
1076 |
|
o pkg/shelfice: |
1077 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
1078 |
|
factor drKp1 to zero where it is negative (ie. do not use |
1079 |
|
SHELFICEBoundaryLayer if hFacC>1) |
1080 |
|
- the same for factor drLoc in shelfice_forcing.F |
1081 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
1082 |
|
with modules in ptracers, when using testreport option "-small_f" |
1083 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
1084 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
1085 |
|
o verification/testreport |
1086 |
|
- add new option -small_f |
1087 |
|
with this option testreport first makes the target small_f (*.f files) |
1088 |
|
before running make (all). This is useful for explicit inlining when |
1089 |
|
all sources need to be full available. |
1090 |
|
o pkg/exf/exf_interp.F: |
1091 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
1092 |
|
|
1093 |
|
checkpoint65k (2015/04/01) |
1094 |
|
o pkg/ecco: |
1095 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
1096 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
1097 |
|
instead of active read/write |
1098 |
|
o pkg/ctrl: |
1099 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
1100 |
|
instead of active read/write. |
1101 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
1102 |
|
return if .NOT.useAUTODIFF |
1103 |
|
o pkg/seaice: add CPP brackets (cost function related). |
1104 |
|
o model/src: |
1105 |
|
add useAUTODIFF run time switch. |
1106 |
|
o pkg/exf/exf_interp.F: |
1107 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
1108 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
1109 |
|
this feature. |
1110 |
|
o verification/testreport: |
1111 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
1112 |
|
implementations of grep that cannot do contextual searches |
1113 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
1114 |
|
of "cat" have the option "-n" |
1115 |
|
o model/src: |
1116 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
1117 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
1118 |
|
convert from conservative to potential temperature. For now they are not |
1119 |
|
called anywhere. |
1120 |
|
o pkg/ggl90: make "useIDEMIX" useful |
1121 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
1122 |
|
are different for idemix into separate loops (changes verification |
1123 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
1124 |
|
- requires 2 new 2D fields KappaM, verticalShear |
1125 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
1126 |
|
s/r ggl90_idemix |
1127 |
|
- fix and improve some comments |
1128 |
|
|
1129 |
|
checkpoint65j (2015/02/25) |
1130 |
|
o pkg/openad |
1131 |
|
- synchronize seawater.F with version in model/src: replace routine |
1132 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
1133 |
|
o pkg/mnc: |
1134 |
|
- change default value of pickup_read/write_mnc params to FALSE |
1135 |
|
(since few features are missing in reading MNC pickup files). |
1136 |
|
o model/src: |
1137 |
|
- change default (background) vertical diffusivity for salt to be the |
1138 |
|
temperature (background) vertical diffusivity. |
1139 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
1140 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
1141 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
1142 |
|
consistent with vertical mixing schemes. |
1143 |
|
o verification/testreport: |
1144 |
|
- fix typo in "-pcls" option ; |
1145 |
|
- put temp files in /tmp (instead of in local dir) |
1146 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
1147 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
1148 |
|
o pkg/ggl90 (idemix code): |
1149 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
1150 |
|
global_ocean.90x40x15.idemix |
1151 |
|
o OpenAD |
1152 |
|
- enable active file I/O and begin removal of work-around code |
1153 |
|
for OpenAD for handling control variables (memory vs. active files) |
1154 |
|
- new CPP options file OPENAD_OPTIONS.h |
1155 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
1156 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
1157 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
1158 |
|
o tools/genmake2: |
1159 |
|
- add option for an alternative Makefile (from Martin) where multiple |
1160 |
|
source files are sent to TAF (instead of all in one file). |
1161 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
1162 |
|
- code provided by Carsten Eden as an extension of ggl90 |
1163 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
1164 |
|
compile time; a runtime flag implementation is not yet complete |
1165 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
1166 |
|
o verification: |
1167 |
|
- reduce length of the AD test run by half for experiments |
1168 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
1169 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
1170 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
1171 |
|
o verification/testreport: |
1172 |
|
- fix two non-POSIX sed statements so that there are no error messages |
1173 |
|
on Mac OS X |
1174 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
1175 |
|
o model/src/seawater.F: |
1176 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
1177 |
|
(following the matlab code), which would have avoided the bug caught |
1178 |
|
by Matt (see below) in the first place |
1179 |
|
o pkg/shelfice: |
1180 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
1181 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
1182 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
1183 |
|
ice-shelf case (i.e., within surface level). |
1184 |
|
- add config summary in shelfice_check.F |
1185 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
1186 |
|
variable recip_latentHeat |
1187 |
|
- introduce diagnostics for friction velocity uStar (in case of |
1188 |
|
SHELFICEuseGammaFrict) |
1189 |
|
- change verification experiment isomip.htd: |
1190 |
|
+ start from pickup (as input_ad at nIter0=8640) |
1191 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
1192 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
1193 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
1194 |
|
o model/src: |
1195 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
1196 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
1197 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
1198 |
|
o pkg/shelfice: |
1199 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
1200 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
1201 |
|
ice-shelf is. |
1202 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
1203 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
1204 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
1205 |
|
for thermodynamic calculations |
1206 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
1207 |
|
affects results of some verification experiments by up to 4 digits: |
1208 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
1209 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
1210 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
1211 |
|
-> updated |
1212 |
|
|
1213 |
|
checkpoint65i (2015/01/23) |
1214 |
|
o model/src: |
1215 |
|
- change units of frictionHeating field from W to W/m^2 |
1216 |
|
- fix bug in frictional heating from stratospheric drag in |
1217 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
1218 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
1219 |
|
field from load_fields_driver.F to thermodynamics.F ; |
1220 |
|
- add diagnostics for frictional heating. |
1221 |
|
o model/src & gmredi K3D: |
1222 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
1223 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
1224 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
1225 |
|
and name in pickup file). |
1226 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
1227 |
|
o model/src: |
1228 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
1229 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
1230 |
|
(since Nov 2012) with option selectAddFluid=1. |
1231 |
|
o pkg/shelfice: |
1232 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
1233 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
1234 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
1235 |
|
o pkg/seaice: two new runtime parameters: |
1236 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
1237 |
|
long overdue |
1238 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
1239 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
1240 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
1241 |
|
for LSR: move checking overlaps out of JFNK-if-block |
1242 |
|
o pkg/atm_phys: |
1243 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
1244 |
|
new S/R ATM_PHYS_DYN2PHYS. |
1245 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
1246 |
|
fixed-in-time pressure levels). |
1247 |
|
o pkg/mom_common (bottomdrag): |
1248 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
1249 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
1250 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
1251 |
|
o pkg/shelfice (u/v_drag): |
1252 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
1253 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
1254 |
|
(now similar to shelfice_u_drag.F) |
1255 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
1256 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
1257 |
|
o pkg/mom_common (bottomdrag): |
1258 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
1259 |
|
- add options for alternative discretisation of velocity norm in quadratic |
1260 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
1261 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
1262 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
1263 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
1264 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
1265 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
1266 |
|
off by default since this also reduces model stability (explicit bottom |
1267 |
|
friction). Changes produce different machine truncation with linear-drag |
1268 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
1269 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
1270 |
|
o model/src & mom pkgs: |
1271 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
1272 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
1273 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
1274 |
|
just copy level Nr value to level Nr+1. |
1275 |
|
o doc: |
1276 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
1277 |
|
o pkg/shelfice: |
1278 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
1279 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
1280 |
|
from array shelficemassinit, which is set in init_fixed and |
1281 |
|
has option to be set from file; introduce array |
1282 |
|
shelficeMassDynTend array, set thru file in init_fixed |
1283 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
1284 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
1285 |
|
pkg/streamice |
1286 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
1287 |
|
SHELFICEMassStepping = .true. |
1288 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
1289 |
|
|
1290 |
|
checkpoint65h (2014/12/17) |
1291 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
1292 |
|
- update to generic controls. |
1293 |
|
o pkg/ctrl: |
1294 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
1295 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
1296 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
1297 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
1298 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
1299 |
|
add time variable weights and cyclic controls (time mean, |
1300 |
|
seasonal cycle, etc) capabilities to gentim2d |
1301 |
|
o pkg/ecco: |
1302 |
|
- move reading of error, conversion to weights from |
1303 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
1304 |
|
o global_oce_llc90, cs32: |
1305 |
|
- activte sbo. |
1306 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
1307 |
|
- activate the new genctrl capabilities. |
1308 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
1309 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
1310 |
|
- add missing ctrl_init_rec.f |
1311 |
|
o tools/OAD_support/keepOriginal: |
1312 |
|
- add ctrl_init_rec.F |
1313 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
1314 |
|
- avoid recomputations of xx_gentim2d_dummy. |
1315 |
|
o momentum diagnostics: |
1316 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
1317 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
1318 |
|
o pkg/seaice/seaice_lsr.F: |
1319 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
1320 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
1321 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
1322 |
|
o verification/global_ocean.cs32x15/input.seaice |
1323 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
1324 |
|
methods for LSR |
1325 |
|
- update results/output.seaice.txt |
1326 |
|
o verification/tutorial_global_oce_biogeo: |
1327 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
1328 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
1329 |
|
update output_adm,_oadm,_tlm.txt |
1330 |
|
o pkg/dic: |
1331 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
1332 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
1333 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
1334 |
|
o verification/tutorial_global_oce_biogeo: |
1335 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
1336 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
1337 |
|
update output_adm,_oadm,_tlm.txt |
1338 |
|
o eesupp/src: |
1339 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
1340 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
1341 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
1342 |
|
LSR (following Hutchings et al. 2004) |
1343 |
|
- introduce zetaZ as a global variable (requires adjustments in |
1344 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
1345 |
|
in seaice_calc_viscosities.F |
1346 |
|
- new flag SEAICEuseStrImpCpl (default off) |
1347 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
1348 |
|
momentum equations |
1349 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
1350 |
|
(where it does not have any positive effect) |
1351 |
|
o pkg/seaice |
1352 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
1353 |
|
turn it off by default (because it only seems to work for non-cubed |
1354 |
|
sphere/llc topologies) |
1355 |
|
o pkg/autodiff |
1356 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
1357 |
|
o pkg/seaice: |
1358 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
1359 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
1360 |
|
o pkg/obcs: |
1361 |
|
- add option to specify domain-connected piece Id along OB though files |
1362 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
1363 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
1364 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
1365 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
1366 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
1367 |
|
o pkg/diagnostics: |
1368 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
1369 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
1370 |
|
outside OB (i.e, where tracer OBCS are applied). |
1371 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
1372 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
1373 |
|
|
1374 |
|
checkpoint65g (2014/11/19) |
1375 |
|
o pkg/diagnostcis: |
1376 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
1377 |
|
o pkg/my82,pp81,kl10: |
1378 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
1379 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
1380 |
|
o pkg/seaice: |
1381 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
1382 |
|
Bouillon et al 2013) |
1383 |
|
- add SEAICE_evpAlpha/Beta to namelist |
1384 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
1385 |
|
involve trivial re-ordering of divisions/multiplications that should not |
1386 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
1387 |
|
that only 2 digits of agreement remain, in line with the general |
1388 |
|
instability/fragility of the evp-code. For now, I do not care and just |
1389 |
|
update the verification experiment |
1390 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
1391 |
|
- remove xx_genarr2d_numsmooth etc |
1392 |
|
- use xx_genarr2d_preproc etc instead |
1393 |
|
- carry out smooth_correl2D at initialization stage rather than during |
1394 |
|
time stepping. |
1395 |
|
- get smoothOpNb from xx_gentim2d_preproc |
1396 |
|
o global_oce_cs32 : |
1397 |
|
- add test of generic ecco capabilities. |
1398 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
1399 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
1400 |
|
o pkg/ctrl,ecco : |
1401 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
1402 |
|
is defined. |
1403 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
1404 |
|
o model/src: |
1405 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
1406 |
|
diffusivity (background) is specified but ignored. |
1407 |
|
o verification: |
1408 |
|
- in testreport, convert hostname to lower case for default output dir name |
1409 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
1410 |
|
o pkg/dic: add modifications from Hajoon: |
1411 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
1412 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
1413 |
|
(read from file). |
1414 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
1415 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
1416 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
1417 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
1418 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
1419 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
1420 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
1421 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
1422 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
1423 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
1424 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
1425 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
1426 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
1427 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
1428 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
1429 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
1430 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
1431 |
|
o pkg/ctrl,ecco,exf : |
1432 |
|
- remove variables associated with NON-generic costs, |
1433 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
1434 |
|
- remove NON-generic NON-obcs controls, |
1435 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
1436 |
|
o pkg/ctrl : added ctrl_local_params.h |
1437 |
|
o pkg/ecco : added ecco_local_params.h |
1438 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
1439 |
|
experiments, which will progressively be removed once the |
1440 |
|
experiments are revised to use only generic controls/costs. |
1441 |
|
|
1442 |
|
checkpoint65f (2014/10/13) |
1443 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
1444 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
1445 |
|
cost function and control capabilities added since checkpoint65c. |
1446 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
1447 |
|
o pkg/ecco: increase modularity and improve logic |
1448 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
1449 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
1450 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
1451 |
|
- cost_gencal.F (new) : determine filnames and records. |
1452 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
1453 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
1454 |
|
and exploit the above functions leading to more compact code. |
1455 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
1456 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
1457 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
1458 |
|
o pkg/ecco: extend generic cost capabilities |
1459 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
1460 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
1461 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
1462 |
|
gencost_outputlevel arguments to cost_generic |
1463 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
1464 |
|
and active_read, making room for gencost_preproc to take effect. |
1465 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
1466 |
|
- pkg/ecco/cost_generic.F : |
1467 |
|
compute and store misfit maks*(model-data) in localdif that is |
1468 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
1469 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
1470 |
|
rather gencost_barfile for deciding whether to write barfile |
1471 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
1472 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
1473 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
1474 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
1475 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
1476 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
1477 |
|
o pkg/ecco: internal re-organization |
1478 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
1479 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
1480 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
1481 |
|
make sure gencost routines only include ecco.h) |
1482 |
|
- throughout : add missing CCP switches, rm unused variables, |
1483 |
|
and rm un-necessary CPP switches |
1484 |
|
- throughout gencost routines : replace modelstartdate with |
1485 |
|
gencost_startdate when needed |
1486 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
1487 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
1488 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
1489 |
|
- ecco_phys.F : compute etanFull |
1490 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
1491 |
|
bpv4-grace to gencost list, initialize added parameters |
1492 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
1493 |
|
|
1494 |
|
checkpoint65e (2014/09/28) |
1495 |
|
o pkg/obcs: |
1496 |
|
- replaced the just-added CPP options with run-time variables |
1497 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
1498 |
|
o pkg/obcs: |
1499 |
|
- add additional CPP options for sponge boundary layers |
1500 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
1501 |
|
o pkg/atm_phys: |
1502 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
1503 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
1504 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
1505 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
1506 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
1507 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
1508 |
|
- implement gentim2d for xx_tauu, xx_tauv |
1509 |
|
o pkg/ctrl, pkg/ecco : |
1510 |
|
- fix and complement the generic controls implementation |
1511 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
1512 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
1513 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
1514 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
1515 |
|
- add weight in CTRL_GET_GEN calls |
1516 |
|
o pkg/ctrl : |
1517 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
1518 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
1519 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
1520 |
|
o pkg/ctrl : |
1521 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
1522 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
1523 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
1524 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
1525 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
1526 |
|
o pkg/ecco, pkg/ctrl : |
1527 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
1528 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
1529 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
1530 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
1531 |
|
|
1532 |
|
checkpoint65d (2014/09/15) |
1533 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
1534 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
1535 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
1536 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
1537 |
|
- remove compilation failure |
1538 |
|
- replace hard coded example |
1539 |
|
- use ctrl_map_ini_gen2D, 3D |
1540 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
1541 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
1542 |
|
o src/packages_init_variables.F : |
1543 |
|
- regroup pkg/estimation calls |
1544 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
1545 |
|
(moved to ctrl_init_variables) |
1546 |
|
o cost/cost_init_varia.F : |
1547 |
|
- remove ecco_cost_init_varia |
1548 |
|
(moved to ecco_init_varia) |
1549 |
|
o ctrl/ctrl_init_variables.F : |
1550 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
1551 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
1552 |
|
o ctrl/ctrl_map_ini.F : |
1553 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
1554 |
|
(moved to ctrl_init_variables) |
1555 |
|
o ctrl/ctrl_map_ini_ecco.F : |
1556 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
1557 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
1558 |
|
o ecco/ecco_ad_diff.list : |
1559 |
|
- add ecco_init_varia.f |
1560 |
|
o ecco/ecco_init_varia.F |
1561 |
|
- new routine |
1562 |
|
o pkg/streamice: |
1563 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
1564 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
1565 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
1566 |
|
o pkg/generic_advdiff: |
1567 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
1568 |
|
o pkg/exf: |
1569 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
1570 |
|
xxg_precip capability |
1571 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
1572 |
|
o pkg/ctrl: |
1573 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
1574 |
|
o model/src/load_fields_driver.F : |
1575 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
1576 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
1577 |
|
o OpenAD verification experiments: |
1578 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
1579 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
1580 |
|
for now, only in pkgs used in OpenAD verification experiments. |
1581 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
1582 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
1583 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
1584 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
1585 |
|
o OpenAD verification tests: |
1586 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
1587 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
1588 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
1589 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
1590 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
1591 |
|
o model/src & generic_advdiff: |
1592 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
1593 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
1594 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
1595 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
1596 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
1597 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
1598 |
|
setting in temp/salt/ptracer_integrate.F |
1599 |
|
o pkg/dic: |
1600 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
1601 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
1602 |
|
in gchem_forcing_sep.F |
1603 |
|
o pkg/autodiff & obcs: |
1604 |
|
- add storage of current OB values for U & V (was already done for T & S). |
1605 |
|
|
1606 |
|
checkpoint65c (2014/08/30) |
1607 |
|
o pkg/dic: |
1608 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
1609 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
1610 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
1611 |
|
o verification: |
1612 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
1613 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
1614 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
1615 |
|
conditions from t=1.yr while keeping the same forcing. |
1616 |
|
o model/src: |
1617 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
1618 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
1619 |
|
o pkg/diagnostics (Stats-Diags): |
1620 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
1621 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
1622 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
1623 |
|
c) extend regional stats over the region edges (for U or V pt location). |
1624 |
|
o pkg/gchem: |
1625 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
1626 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
1627 |
|
o verification (hs94): |
1628 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
1629 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
1630 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
1631 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
1632 |
|
o pkg/ptracers: |
1633 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
1634 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
1635 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
1636 |
|
with AB-2 code (so that it get tested). |
1637 |
|
o model/src: |
1638 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
1639 |
|
with AB-2 code (previously only available with AB-3 code). |
1640 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
1641 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
1642 |
|
there, by calling CYCLE_AB_TRACER). |
1643 |
|
o pkg/generic_advdiff: |
1644 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
1645 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
1646 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
1647 |
|
S/R temp/salt/ptracers_integrate.F |
1648 |
|
o model/src & pkg/ptracers: |
1649 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
1650 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
1651 |
|
- remove common block variable gPtr. |
1652 |
|
o model/src & pkgs: |
1653 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
1654 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
1655 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
1656 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
1657 |
|
+ change accordingly all calling S/R. |
1658 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
1659 |
|
in S/R temp/salt/ptracers_integrate.F |
1660 |
|
o pkg/seaice: |
1661 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
1662 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
1663 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
1664 |
|
in seaice_lsr |
1665 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
1666 |
|
in s/r seaice_lsr_calc_coeffs |
1667 |
|
o pkg/mdsio: |
1668 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
1669 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
1670 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
1671 |
|
|
1672 |
|
checkpoint65b (2014/08/12) |
1673 |
|
o pkg/matrix: |
1674 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
1675 |
|
o model/src: |
1676 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
1677 |
|
natl_box verification experiment. |
1678 |
|
o model/src & pkg/down_slope: |
1679 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
1680 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
1681 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
1682 |
|
results at machine truncation level: update output of experiments |
1683 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
1684 |
|
o pkg/diagnostics (Stats-Diags): |
1685 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
1686 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
1687 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
1688 |
|
times (but Min,Max and StD are still wrong). |
1689 |
|
o model/src: |
1690 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
1691 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
1692 |
|
o model/src: |
1693 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
1694 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
1695 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
1696 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
1697 |
|
o model/src: |
1698 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
1699 |
|
anomaly that is used to compute geopotential: this make the atmos code |
1700 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
1701 |
|
o pkg/seaice/seaice_lsr.F |
1702 |
|
- rename integer variable ilcall to ipass (that's what it is called |
1703 |
|
in the residual diagnostics |
1704 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
1705 |
|
default) for improved non-linear convergence of the first few steps |
1706 |
|
- adjust a few comments and add new ones to explain some of the store |
1707 |
|
directives |
1708 |
|
o pkg/generic_advdiff (& ptracers): |
1709 |
|
- re-work the code to check for valid advection scheme and for minimum |
1710 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
1711 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
1712 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
1713 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
1714 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
1715 |
|
less exact gradients in my tests); but there are still |
1716 |
|
recomputation warning (although gradients are sort of OK), when |
1717 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
1718 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
1719 |
|
- update verification experiments lab_sea. |
1720 |
|
- change some comments in S/R seaice_calc_viscosities |
1721 |
|
o model/src: |
1722 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
1723 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
1724 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
1725 |
|
but affects AD results (at machine truncation level): update output of |
1726 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
1727 |
|
and isomip (oad: 12.d). |
1728 |
|
o pkg/generic_advdiff: |
1729 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
1730 |
|
- refine warning related to stability of tracer time-stepping |
1731 |
|
regarding internal wave dynamics. |
1732 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
1733 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
1734 |
|
if potentially unstable). |
1735 |
|
o pkg/kl10: |
1736 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
1737 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
1738 |
|
(contribution from Jody Klymak), tested in verification experiment |
1739 |
|
verification/internal_wave/input.kl10/ |
1740 |
|
o isomip experiment: |
1741 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
1742 |
|
(input.htd) and update the output. |
1743 |
|
o cd_code experiments: |
1744 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
1745 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
1746 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
1747 |
|
update the corresponding output. |
1748 |
|
o pkg/seaice: |
1749 |
|
- reduce the number of include files and store directives in |
1750 |
|
S/R seaice_lsr_tridiagu/v |
1751 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
1752 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
1753 |
|
get rid off one store directive (a TAF bug?) |
1754 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
1755 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
1756 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
1757 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
1758 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
1759 |
|
offline_exf_seaice/input.dyn_jfnk) |
1760 |
|
|
1761 |
|
checkpoint65a (2014/07/27) |
1762 |
|
o model/src: |
1763 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
1764 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
1765 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
1766 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
1767 |
|
o model/src: |
1768 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
1769 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
1770 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
1771 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
1772 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
1773 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
1774 |
|
affects results at machine truncation level (e.g., ocean: if using |
1775 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
1776 |
|
correction due to vertical advection). |
1777 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
1778 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
1779 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
1780 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
1781 |
|
o pkg/ptracers & diagnostics: |
1782 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
1783 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
1784 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
1785 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
1786 |
|
|
1787 |
checkpoint65 (2014/07/18) |
checkpoint65 (2014/07/18) |
1788 |
o pkg/fizhi: |
o pkg/fizhi: |
1789 |
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
1802 |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
1803 |
this experiment): |
this experiment): |
1804 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
1805 |
text data bss dec hex |
text data bss dec hex |
1806 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
1807 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
1808 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
1809 |
text data bss dec hex |
text data bss dec hex |