4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o tools/xmakedepend: |
8 |
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- In case line editor "ed" is missing, switch to "sed" command to clean-up |
9 |
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Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
10 |
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o pkg/exf: |
11 |
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- change definition of "hflux" input file to always include Short-Wave; |
12 |
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this is now consistent with hflux computation (if using bulk-formulae) |
13 |
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and hflux diagnostic & documentation (in EXF_FIELDS.h). |
14 |
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|
15 |
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checkpoint66b (2016/12/01) |
16 |
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o model & momentum pkgs: |
17 |
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- implement fully implicit bottom friction combined with implicit surf. |
18 |
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pressure, for now, only in hydrostic formulation: |
19 |
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+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
20 |
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and run with selectImplicitDrag=2 ; |
21 |
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+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
22 |
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- partial implicit time-stepping (bot. friction + vert. visc first, then |
23 |
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surf. press) corresponding to selectImplicitDrag=1 should be applicable |
24 |
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to NH formulation but not available until we solve for surf. pressure |
25 |
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increment (instead of full etaN). |
26 |
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- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
27 |
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with implicit vertical viscosity. |
28 |
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o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
29 |
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- this is a first version that includes many regularisations that may |
30 |
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not all be necessary, to be sorted out, |
31 |
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- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
32 |
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- change one verification experiment in seaice_itd to use and test new code |
33 |
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- seaice_growth: catch a case where the argument of log can be zero |
34 |
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or smaller (important for code stability) |
35 |
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o model/src: |
36 |
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- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
37 |
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& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
38 |
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similar A.X'=Y' system (with same matrix A) in subsequent calls; |
39 |
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switch based on errCode (In/Out) argument value; in calling routines, |
40 |
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initialise errCode before first call. |
41 |
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|
42 |
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checkpoint66a (2016/10/18) |
43 |
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o pkg/bling: |
44 |
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- BLING package now loads in atmospheric pCO2 file using exf package routines |
45 |
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Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
46 |
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o model/src & pkg/ptracers: |
47 |
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- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
48 |
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GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
49 |
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implicitDiffusion (respectively) are used (even without momImplVertAdv |
50 |
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or temp,salt,PTRACERS_ImplVertAdv). |
51 |
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o model/src & generic_advdiff: |
52 |
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- add parenthesis in main diagonal calculation of implicit vertical |
53 |
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diffusion matrix (impldiff.F & gad_implicit_r.F). |
54 |
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This affects results at machine truncation level; update output of many |
55 |
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verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
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o pkg/mom_commom & generic_advdiff: |
57 |
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- add deep atmosphere and anelastic scaling factor in implicit vertical |
58 |
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advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
59 |
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o model/src: |
60 |
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- remove few unnecessary temp array copies in solve_tridiagonal.F |
61 |
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& solve_pentadiagonal.F |
62 |
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|
63 |
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checkpoint65z (2016/09/28) |
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o pkg/seaice: fix multithreading for seaice_fgmres.F |
65 |
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- remove unecessary variables from common blocks |
66 |
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- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
67 |
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basis, that are stored in commom blocks (including integer variable i1) |
68 |
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- clean up code a little by removing commented lines that refer to |
69 |
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original code |
70 |
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- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
71 |
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o MITgcm manual: |
72 |
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- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
73 |
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preliminary documentation for generic controls (8.3; ctrl.tex), |
74 |
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a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
75 |
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ecco_costfunction.tex |
76 |
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o pkg/ecco: |
77 |
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- update and cleanup list of CCP options |
78 |
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- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
79 |
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is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
80 |
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- add checks that retired run-time options are not used, and in relation |
81 |
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to gencost_mask and gencost_errfile |
82 |
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- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
83 |
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gencost_nrecperiod |
84 |
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- fix m_eta computation for virtual salt flux case |
85 |
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- add m_horflux_vol case (selected via gencost_barfile) that computes |
86 |
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transports via cost_gencost_boxmean (gencost_flag=-3) |
87 |
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- use gencost_flag more systematically (i.e., avoid using gencost_name) |
88 |
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for code switches (aside from physical variable selection) |
89 |
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o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
90 |
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attempt appears to be a bit of a hack and my need some repair down the road |
91 |
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o pkg/exf: |
92 |
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- interpolation near South Pole: fix criteria on input field latitude. |
93 |
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o pkg/icefront & pkg/exf: |
94 |
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- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
95 |
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from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
96 |
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o pkg/exf: |
97 |
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- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
98 |
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"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
99 |
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(add suffix "_out" instead of a prefix); keep same record number as in |
100 |
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input file but always write record 1 first (to avoid a STOP in I/O S/R). |
101 |
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Change output file content by writing interpolated field before applying |
102 |
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land-sea mask (helpful for debug). |
103 |
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- 2 compon. vector interpolation with rotation: apply scaling factor on |
104 |
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each compon. (Eastward and Northward) just before rotation. |
105 |
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o pkg/bling: |
106 |
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- Cleaned package. Removed not needed code and comments. |
107 |
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- adjoint example now works |
108 |
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(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
109 |
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o pkg/ptracers: |
110 |
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- add Bruno Deremble's code to complete the linear surface correction |
111 |
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for tracer conservation; |
112 |
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- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
113 |
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|
114 |
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checkpoint65y (2016/07/29) |
115 |
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o pkg/debug (stats): |
116 |
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- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
117 |
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proc/thread mapping); |
118 |
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- fix Min & Max for case where 1 thread has only empty tiles; |
119 |
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- use RL variable to count number of wet grid points (with big domain, |
120 |
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can be too large to fit into integer*4). |
121 |
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o pkg/monitor: |
122 |
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- use RL variable to count number of wet grid points (but used only for del2) |
123 |
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- add new routine to compute Advective CFL within tracer time-stepping with |
124 |
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writing delayed until next monitor output. |
125 |
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o pkg/obcs: |
126 |
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- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
127 |
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o pkg/cal: |
128 |
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- calandar-dump: treat case myTime < timePhase in the same way as in |
129 |
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eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
130 |
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o pkg/dic & seaice: |
131 |
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- fix compilation of ocean component for coupled atm+ocn model with |
132 |
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seaice dynamics & dic. |
133 |
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|
134 |
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checkpoint65x (2016/06/11) |
135 |
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o add a license text file in main MITgcm tree. |
136 |
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o added pkg/bling: |
137 |
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- intermediate complexity biogeochemical model |
138 |
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- see bling_description.txt for details |
139 |
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- verification experiment is global_oce_biogeo_bling (for now, in |
140 |
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Contrib/verification_other/); tested daily on baudelaire with gfortran. |
141 |
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- add entry point in pkg/gchem for new pkg "bling". |
142 |
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o pkg/seaice: fix tensile stength computation |
143 |
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- replace global field tensileStrength by tensileStrFac |
144 |
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- tensileStrFac can be computed once in S/R seaice_init_varia |
145 |
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- fortunately that does not affect any verification results |
146 |
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|
147 |
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checkpoint65w (2016/05/12) |
148 |
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o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
149 |
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with ECCO_CTRL_DEPRECATED defined |
150 |
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o verification/global_ocean.cs32x15: |
151 |
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- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
152 |
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with "selectNHfreeSurf=1". |
153 |
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o model/src (non-hydrostatic free-surface): |
154 |
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- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
155 |
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was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
156 |
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- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
157 |
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for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
158 |
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and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
159 |
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This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
160 |
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- Update output (changes at machine truncation level) of verification exp: |
161 |
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exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
162 |
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short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
163 |
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o pkg/seaice: ITD code |
164 |
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- fix picking up from a single category model by initialising |
165 |
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heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
166 |
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- split a long warning message in seaice_check_pickup.F into two lines, |
167 |
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because NEC SX-ACE cannot deal with the long line. |
168 |
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o model/src: |
169 |
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- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
170 |
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o pkg/seaice: |
171 |
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- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
172 |
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o pkg/seaice: |
173 |
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- add basal stress as parameterisation for grounding ice |
174 |
|
following Lemieux et al. (2015) |
175 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
176 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
177 |
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- The adjoint complains with extra recomputations so there is also a |
178 |
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new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
179 |
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order to postpone the problem |
180 |
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- compile the new code in lab_sea |
181 |
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o verification/halfpipe_streamice: |
182 |
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- update both TAF and OpenAD adm output (machine truncation differences) |
183 |
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|
184 |
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checkpoint65v (2016/04/08) |
185 |
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o verification/advect_xz: |
186 |
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- increase overlap size from 3 to 4 and add new secondary test for PQM |
187 |
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advection scheme (with mono & wino limiter). |
188 |
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- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
189 |
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o model/src: |
190 |
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- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
191 |
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added phi0Ref) to set vertical axis origin and phiRef origin; |
192 |
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keep Ro_SeaLevel for backward compatibility (with a warning). |
193 |
|
According to coordinate and fluid type: |
194 |
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OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
195 |
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ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
196 |
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OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
197 |
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ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
198 |
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- remove Ro_SeaLevel from ATM experiment parameter files; |
199 |
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- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
200 |
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complement; update output.txt (changes at machine truncation level). |
201 |
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o pkg/seaice/seaice_evp.F |
202 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
203 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
204 |
|
verification experiment lab_sea.hb87 -> updated |
205 |
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|
206 |
|
checkpoint65u (2016/03/14) |
207 |
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o pkg/generic_advdiff: |
208 |
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- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
209 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
210 |
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Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
211 |
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testing and not for actual use. |
212 |
|
o model/src: |
213 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
214 |
|
origin r = rF(1); |
215 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
216 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
217 |
|
more accurate pressure vertical profile; options not linked to EOS type |
218 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
219 |
|
- start to implement variable gravity (along vertical): for now, only with |
220 |
|
z-coords (not even z*). |
221 |
|
- add Ideal Gas equation of state for height coordinate. |
222 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
223 |
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global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
224 |
|
o pkg/exf: |
225 |
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- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
226 |
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of exf interpolation (before any rescaling, rotation or interpolation |
227 |
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to velocity point) for each field that gets loaded from file. This option |
228 |
|
identically mimics the input file organization (e.g. record numbers in year |
229 |
|
by year input files) besides the change in horizontal grid. |
230 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
231 |
|
can be provided on the A-grid in zonal/meridional direction and |
232 |
|
rotated on the fly. This only applies to the case when the exf |
233 |
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interpolation is off and rotateStressOnAgrid is false by default. |
234 |
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o model/src: |
235 |
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- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
236 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
237 |
|
inactive, src code yet to come) |
238 |
|
|
239 |
|
checkpoint65t (2016/02/10) |
240 |
|
o pkg/atm_phys: |
241 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
242 |
|
o model/src: |
243 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
244 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
245 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
246 |
|
o tools: |
247 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
248 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
249 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
250 |
|
o pkg/seaice: |
251 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
252 |
|
has an effect |
253 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
254 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
255 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
256 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
257 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
258 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
259 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
260 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
261 |
|
use with SEAICEuseKrylov |
262 |
|
o pkg/seaice/seaice_lsr.F |
263 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
264 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
265 |
|
an effect. |
266 |
|
o pkg/seaice: add two new parameters |
267 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
268 |
|
parameter is not in any namelist) |
269 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
270 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
271 |
|
solver |
272 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
273 |
|
affects some experiments at truncation level: |
274 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
275 |
|
- global_ocean.cs32x15.seaice (11 digits), |
276 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
277 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
278 |
|
o pkg/salt_plume & pkg/thsice: |
279 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
280 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
281 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
282 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
283 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
284 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
285 |
|
o pkg/dic: |
286 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
287 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
288 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
289 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
290 |
|
(previously done in ocn_apply_import.F). |
291 |
|
o tools/adjoint_options: |
292 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
293 |
|
has been changed on Jan 14, 2016. |
294 |
|
o pkg/ggl90: |
295 |
|
- add alternative discretisation of vertical shear (off by default), to |
296 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
297 |
|
vertical shear of mean flow (@ grid-cell center). |
298 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
299 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
300 |
|
o pkg/atm_compon_interf: |
301 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
302 |
|
pass last value, stored directly before export to CPL ; |
303 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
304 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
305 |
|
|
306 |
|
checkpoint65s (2016/01/13) |
307 |
|
o eesupp & genmake2: |
308 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
309 |
|
ETIME and consistent output; use the appropriate version in timers.F |
310 |
|
o model/src: |
311 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
312 |
|
integr_continuity; turned off by default. |
313 |
|
o pkg/dic: |
314 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
315 |
|
o tools/tst_2+2: |
316 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
317 |
|
to fail for no good reason. |
318 |
|
o eesupp & genmake2: |
319 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
320 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
321 |
|
o coupler pkgs: |
322 |
|
Finish implementation of optionally-exchanged variable switches (started on |
323 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
324 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
325 |
|
advection in OCN component; this requires sequential coupling. |
326 |
|
coupler (pkg/atm_ocn_coupler): |
327 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
328 |
|
routines (useful for debug). |
329 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
330 |
|
flux, DIC fields) if corresponding switch is ON. |
331 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
332 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
333 |
|
components (pkg/atm_ & ocn_compon_interf): |
334 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
335 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
336 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
337 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
338 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
339 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
340 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
341 |
|
- hold in common block coupler optionally-exchanged variable switch |
342 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
343 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
344 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
345 |
|
to contain new additional exchanged fields). |
346 |
|
o pkg/dic: |
347 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
348 |
|
o pkg/thsice: |
349 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
350 |
|
and writing of thsice pickup files. |
351 |
|
o pkg/atm_compon_interf: |
352 |
|
- move all field individual export-call out of cpl_export_import_data.F |
353 |
|
into new S/R ATM_EXPORT_FIELDS |
354 |
|
o pkg/atm_compon_interf: |
355 |
|
- store state variables (for now, only thSIce fields) just before beeing |
356 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
357 |
|
atm_store_my_data.F like all exported fluxes. |
358 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
359 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
360 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
361 |
|
o pkg/dic: |
362 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
363 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
364 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
365 |
|
value can be from domain [0,1] to average between the two methods |
366 |
|
o pkg/atm_phys: |
367 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
368 |
|
hold fixed in time). |
369 |
|
|
370 |
|
checkpoint65r (2015/12/21) |
371 |
|
o pkg/seaice: |
372 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
373 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
374 |
|
o pkg/seaice: |
375 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
376 |
|
when SEAICEscaleSurfStress=.TRUE., |
377 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
378 |
|
o pkg/atm_phys: |
379 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
380 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
381 |
|
for individual contribution (convection, LSC cond, radiation) |
382 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
383 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
384 |
|
o pkg/ggl90: |
385 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
386 |
|
avoid instability problems in the explicit horizontal diffusion term for |
387 |
|
long time steps or high resolution |
388 |
|
o pkg/diagnostics: |
389 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
390 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
391 |
|
o testreport: |
392 |
|
- remove "-v" (verbose option) in default mpirun command. |
393 |
|
o pkg/seaice/seaice_growth: |
394 |
|
- catch potential division by zero in ITD code, does not change |
395 |
|
verification results |
396 |
|
o pkg/ecco: |
397 |
|
- retire old codes to the Attic. The calls to retired functions are |
398 |
|
left in a commented form in case they ever need to be re-activated. |
399 |
|
- ecco_check.F: issue warning if any old CPP option is |
400 |
|
defined that corresponds to retired codes -- then stop. |
401 |
|
o pkg/atm_compon_interf: |
402 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
403 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
404 |
|
time-step, similar to what is done for seaIceMass. |
405 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
406 |
|
o eesupp & genmake2: |
407 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
408 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
409 |
|
o pkg/seaice/seaice_evp: |
410 |
|
- refine residual computation |
411 |
|
|
412 |
|
checkpoint65q (2015/11/18) |
413 |
|
o pkg/seaice/seaice_evp: |
414 |
|
- fix residual computations so that they no longer affect the actual |
415 |
|
simulation code |
416 |
|
- fix seaice_readparams to be able to actually set new parameters |
417 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
418 |
|
o model/src: |
419 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
420 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
421 |
|
a) replaced by DFLOAT (if not seen by TAF); |
422 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
423 |
|
o pkg/aim_v23: |
424 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
425 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
426 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
427 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
428 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
429 |
|
add corresponding call in DO_OCEANIC_PHYS. |
430 |
|
o coupler pkgs: |
431 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
432 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
433 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
434 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
435 |
|
compononent param default can be set accordingly). |
436 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
437 |
|
but rather applies to a group a fields (going both ways like for DIC) |
438 |
|
and corresponds to an option of coupling config. |
439 |
|
coupler (pkg/atm_ocn_coupler): |
440 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
441 |
|
and read namelist directly (without eessup S/R calls) instead of |
442 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
443 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
444 |
|
cleanly in CPL_CHECK_CPLCONFIG |
445 |
|
- add new coupling-exchange selectors (some not yet active) including |
446 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
447 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
448 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
449 |
|
component ; called directly from coupler.F, after comp. registrations; |
450 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
451 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
452 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
453 |
|
components (pkg/atm_ & ocn_compon_interf): |
454 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
455 |
|
CPP header file in all pkg source files. |
456 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
457 |
|
ATM/OCN_CHECK_CPLCONFIG; |
458 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
459 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
460 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
461 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
462 |
|
before PACKAGES_READPARMS; |
463 |
|
verification/cpl_aim+ocn/: |
464 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
465 |
|
"data.cpl" for coupler (in input_cpl). |
466 |
|
o eesupp/inc: |
467 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
468 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
469 |
|
to always cumulate tile local-sum in the same order (still uses |
470 |
|
MPI_Allreduce like standard code). |
471 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
472 |
|
that are now identical to standard version (in eesupp/inc). |
473 |
|
o pkg/shelfice: |
474 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
475 |
|
heat and salt transfer coefficients |
476 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
477 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
478 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
479 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
480 |
|
o pkg/atm_ocn_coupler: |
481 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
482 |
|
o pkg/rbcs: |
483 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
484 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
485 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
486 |
|
|
487 |
|
checkpoint65p (2015/10/23) |
488 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
489 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
490 |
|
solution, but at least there are no more recomputation warnings left |
491 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
492 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
493 |
|
o tools/adjoint_options/adjoint_diva: |
494 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
495 |
|
o pkg/streamice: |
496 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
497 |
|
o pkg/exf: |
498 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
499 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
500 |
|
o pkg/seaice: |
501 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
502 |
|
5 additionals 2D fields and 6 new store directives |
503 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
504 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
505 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
506 |
|
or SEAICEaEVPcoeff |
507 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
508 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
509 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
510 |
|
- this is an intermediate state of a truely converging EVP that has |
511 |
|
the potential of outperforming implicit VP methods, I do not recommend |
512 |
|
using it yet. |
513 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
514 |
|
and all parameters are hardwired |
515 |
|
- for convergence it still requires very smooth regularisations, that means, |
516 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
517 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
518 |
|
specific averaging appears to be required, still subject to tuning |
519 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
520 |
|
- add code to compute and print residuals of iteration, compile with |
521 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
522 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
523 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
524 |
|
|
525 |
|
checkpoint65o (2015/09/14) |
526 |
|
o pkg/mom_vecinv & mom_common: |
527 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
528 |
|
called from there. |
529 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
530 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
531 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
532 |
|
and Koenig-Beatty+Holland (2012) |
533 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
534 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
535 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
536 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
537 |
|
(to be changed and played with, for now exponential) |
538 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
539 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
540 |
|
by AREA according to Connelly et al. (2004), JPO. |
541 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
542 |
|
the only non-zero term in the denominator when there is no ice (which |
543 |
|
prevented running the model with zero ice-ocean drag). If |
544 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
545 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
546 |
|
consequence is that for open water, the momentum equation reduce |
547 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
548 |
|
they happen to be zero, often leading to a non-zero solution over |
549 |
|
open water. |
550 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
551 |
|
efficient EVP method. |
552 |
|
- introduce area-weighted averages for e12 (analogously to |
553 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
554 |
|
remain, but also changing the order of terms in the previous average |
555 |
|
changed the results as much) -> update experiment |
556 |
|
- add SEAICE_DELTA_SMOOTHREG code |
557 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
558 |
|
TEM-code |
559 |
|
- adjust loop bounds so that only required fields are computed |
560 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
561 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
562 |
|
results again), but will replace old code eventually |
563 |
|
o eesupp/src: |
564 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
565 |
|
to always cumulate tile local-sum in the same order |
566 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
567 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
568 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
569 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
570 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
571 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
572 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
573 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
574 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
575 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
576 |
|
|
577 |
|
checkpoint65n (2015/07/29) |
578 |
|
o pkg/thsice: |
579 |
|
- add a warning when used with pkg/aim but without updating SST |
580 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
581 |
|
o pkg/offline: |
582 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
583 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
584 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
585 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
586 |
|
These changes allow: |
587 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
588 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
589 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
590 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
591 |
|
b) no needs to switch on staggerTimeStep anymore; |
592 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
593 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
594 |
|
o pkg/offline: |
595 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
596 |
|
can easily recover previous offset-iter effect by setting offset-time |
597 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
598 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
599 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
600 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
601 |
o OpenAD |
o OpenAD |
602 |
- Adding preliminary ggl90 test to OpenAD verification. |
- Adding preliminary ggl90 test to OpenAD verification. |
603 |
Config. with ggl90 currently diverges after 64 time steps |
Config. with ggl90 currently diverges after 64 time steps |
604 |
so will need more work to become more stable |
so will need more work to become more stable |
605 |
- Adding preliminary kpp test to OpenAD verification. |
- Adding preliminary kpp test to OpenAD verification. |
606 |
required small tweakes in kpp_routines.F |
required small tweakes in kpp_routines.F |
607 |
- Merge and update from Krishna Narayanan's contrib area: |
- Merge and update from Krishna Narayanan's contrib area: |
608 |
* Add one variable for preliminary OpenAD DIVA |
* Add one variable for preliminary OpenAD DIVA |
609 |
* Add replacement time-stepping for OpenAD DIVA |
* Add replacement time-stepping for OpenAD DIVA |
610 |
* genmake2 flag -diva (but only for OpenAD; preliminary) |
* genmake2 flag -diva (but only for OpenAD; preliminary) |
611 |
* required modifs for OAD_support |
* required modifs for OAD_support |
612 |
successful preliminary test for tutorial_global_oce_biogeo/ |
successful preliminary test for tutorial_global_oce_biogeo/ |
613 |
|
o pkg/seaice: |
614 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
615 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
616 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
617 |
|
(no effect on EVP) |
618 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
619 |
o pkg/seaice: |
o pkg/seaice: |
620 |
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
add new parameter SEAICE_deltaMin that is used ***only*** |
621 |
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
for regularizing Delta (and nothing else, like the parameter |
622 |
delta with a smooth function in s/r seaice_calc_viscosity |
which is also used for all sorts of things SEAICE_EPS). |
623 |
(no effect on EVP) |
Defaults to SEAICE_EPS for backward compatibility only. |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
|
|
o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only*** |
|
|
for regularizing Delta (and nothing else, like the parameter |
|
|
which is also used for all sorts of things SEAICE_EPS). Defaults to |
|
|
SEAICE_EPS for backward compatibility only. |
|
624 |
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
625 |
the wrong key by inialising it before use -> fixes a recomputation |
the wrong key by inialising it before use -> fixes a recomputation |
626 |
problem but does not fix the gradient |
problem but does not fix the gradient |
627 |
o pkg/layers: |
o pkg/layers: |
628 |
- move resetting of flux arrays to outside the iLa loop |
- move resetting of flux arrays to outside the iLa loop |
629 |
(this caused layers_diapycnal to not work with more than one layer coord.) |
(this caused layers_diapycnal to not work with more than one layer coord.) |
635 |
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
636 |
in lab_sea forward experiment (changes results -> updated) |
in lab_sea forward experiment (changes results -> updated) |
637 |
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
638 |
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
639 |
computations; for SEAICE_VECTORIZE_LSR |
computations; for SEAICE_VECTORIZE_LSR |
640 |
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
641 |
sweep to the outside, |
sweep to the outside, |
642 |
- remove store directives and add "CADJ loop sequential" directives |
- remove store directives and add "CADJ loop sequential" directives |
902 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
903 |
o doc: |
o doc: |
904 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
905 |
o pkg/streamice: |
o pkg/shelfice: |
906 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
907 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
908 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |