4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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o pkg seaice |
8 |
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- re-introduce global field frWtrAtm for the case of |
9 |
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ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F) |
10 |
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- catch the case of an empty filename in seaice_cost_init_fixed.F |
11 |
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o pkg ecco: |
12 |
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- small bug fixes in the_main_loop |
13 |
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. fix order of monitor arguments |
14 |
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. change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY |
15 |
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. move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so |
16 |
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that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF |
17 |
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- replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the |
18 |
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imbalance diagnostics for wmean_h/sflux = 0 |
19 |
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- add actual values to f_obcsn/s/w/e in ecco_cost_final.F |
20 |
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- catch the case of empty filenames in ecco_cost_init_fixed.F |
21 |
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and ecco_readparms.F |
22 |
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- fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta) |
23 |
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to make this statement meaningfull |
24 |
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o pkg zonal_filt: |
25 |
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- change ZONAL_FILTER S/R interface (allows to filter 2-D fields) |
26 |
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- when using rStar, filter uVel*hFacW instead of uVel |
27 |
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(tested without topography: fix a Pb of growing instability with NLFS) |
28 |
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o pkg/aim/thsice: |
29 |
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-Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F |
30 |
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(works as SST restoring) |
31 |
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o pkg/thsice: |
32 |
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-add specific parameter for salt restoring in slab mixed-layer |
33 |
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(by default equal to the temperature restoring) |
34 |
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|
35 |
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checkpoint61v |
36 |
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o pkg/kpp: |
37 |
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-add double diffusive contributions as a hack, turned off by default |
38 |
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for now, and the code can be excluded with a CPP-flag |
39 |
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EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX |
40 |
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-add a verification experiments to "vermix" to test this code |
41 |
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o pkg/mom_common: |
42 |
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Move computation of length scales to mom_init_fixed.F (avoid recomputation |
43 |
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at each time-steps*levels). |
44 |
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o pkg/layers: |
45 |
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Created a new package for computing volume fluxes in temperature or |
46 |
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[not yet implemented] density layers, e.g. for calculating residual |
47 |
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overturning circulations. |
48 |
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o pkg/diagnostics: |
49 |
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implement a RS type version for the set of DIAGNOSTICS-FILL subroutines |
50 |
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o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option) |
51 |
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o pkg/mdsio (& pkg/rw): rework high level S/R interface: |
52 |
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To avoid mixing type (RS/RL) of input/output array argument, |
53 |
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replace single mixed-type array with a pair from each type (RS/RL). |
54 |
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o setting pickupSuff force to start from a pickup (even if nIter0=0): this |
55 |
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is now implemented for all pkgs (previously only done for the main pickup) |
56 |
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|
57 |
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checkpoint61u |
58 |
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o pkg/obcs: |
59 |
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- change OB?eta from _RS to _RL and put them into a separate commen block |
60 |
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- add code to read OB?eta from a file via obcs_prescribe_read: the code |
61 |
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compiles and does not destroy any other experiments, the data is read |
62 |
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properly, but the code is not tested in actual applications |
63 |
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o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to |
64 |
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create a meaningful unit attribute for the time coordinate variable |
65 |
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o pkg/ebm: add plenty of missing "_d 0" ; |
66 |
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update results of experiment global_ocean_ebm (fwd + adjoint tests) |
67 |
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Notes: several pieces of code only works for (very) specific set up |
68 |
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(domain size, lat range, etc ...); should be documented & stop if one |
69 |
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of those assumptions is not meet. |
70 |
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o pkg/seaice: add missing "_d 0" in HSNOW initialisation |
71 |
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update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests) |
72 |
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and offline_exf_seaice (seaicetd + adjoint). |
73 |
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o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC): |
74 |
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update results of experiments: lab_sea (4 fwd tests + 3 adjoint), |
75 |
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seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2). |
76 |
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o few changes to pass when compiling with strick checking of arguments |
77 |
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across S/R (allow to find few bugs in S/R calls). |
78 |
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o pkg/seaice: |
79 |
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- seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new |
80 |
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2d-fields, for slightly better performance |
81 |
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|
82 |
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checkpoint61t |
83 |
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o pkg/seaice: |
84 |
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- remove unused variables in seaice_evp |
85 |
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- reduce number of SQRT in seaice_evp and seaice_calc_viscosities |
86 |
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o eeset_parms.F, open_copy_data_file.F & ini_parms.F: |
87 |
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named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT): |
88 |
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each processor opens a different file (a fix from Matt). |
89 |
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o cg2d: |
90 |
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use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F : |
91 |
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this reduces number of EXCH calls by 2 when using exch2. |
92 |
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For now, keep previous size array for gc2d_nsa.F to avoid Pb with store |
93 |
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directives and missing simple EXCH (exch_s3d_rx) adjoint code. |
94 |
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o pkg/thsice: |
95 |
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add code for Near Infra-Red albedo (from Jeff) |
96 |
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(turned on with run-time flag: thSIce_calc_albNIR, in data.ice). |
97 |
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o ini_model_io: |
98 |
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move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F |
99 |
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MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F |
100 |
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to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice. |
101 |
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|
102 |
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checkpoint61s |
103 |
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o pkg/exch2 (exch2_rxN_cube*): |
104 |
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remove last BARRIER (no need to synchronise after getting data from shared |
105 |
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buffer (get) as long as any change to buffer (put,recv) is between BARRIER) |
106 |
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o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH |
107 |
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and generate new output (for the 2 tests) using default rotationPeriod. |
108 |
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o pkg/exch2: |
109 |
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- always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F |
110 |
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(was already the case with AUTODIFF_EXCH2 defined) |
111 |
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- add bj in exch2 arrays and S/R. |
112 |
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- can now use pkg/exch2 for regular (non CS) set-up; switch test experiment |
113 |
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MLAdjust to exch2 (identical results except with MPI -> truncation diff); |
114 |
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o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep |
115 |
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- adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY |
116 |
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GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT |
117 |
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- verification experiment natl_box.longstep |
118 |
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o build_options: ifort+mpi_aces optfile (following Constantinos advise): |
119 |
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allow different versions of ifort (8 or 9) and different versions |
120 |
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of mpi (mpich or mpich2) to be used with the same optfile. |
121 |
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requires to load a netcdf module and set MPI_INC_DIR (see comments inside |
122 |
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optfile). Change testing scripts (example_scripts/ACESgrid) accordingly. |
123 |
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o pkg/seaice: |
124 |
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fix previous modif (3-level field removed) for old-pickup reading |
125 |
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|
126 |
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checkpoint61r |
127 |
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o pkg/seaice: |
128 |
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- clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps: |
129 |
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1. introduce fields for time step (N-1) |
130 |
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2. do not use levels 2 and 3 anymore (but keep them) |
131 |
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3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This |
132 |
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includes changes to pkg/thsice/thsice_get_velocity.F, |
133 |
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model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and |
134 |
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pkg/obcs/obcs_apply_uvice.F. |
135 |
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- completely remove code for leap-frog time stepping for second order |
136 |
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advection |
137 |
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- adjusted adjoint accordingly; |
138 |
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gradient checks have improved by an order of magnitude! |
139 |
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|
140 |
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checkpoint61q |
141 |
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o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver |
142 |
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- the boundary conditions along open boundaries are unclear, because the |
143 |
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associated masks are set to zero and are thus treated as closed when |
144 |
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applying the slip-boundary conditions. |
145 |
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- move initialisation of grid variables from seaice_init_varia to _fixed |
146 |
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o adding doc/diags_changes.txt |
147 |
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o model/src: |
148 |
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do_the_model_io: rename few pkg S/R which are called from do_the_model_io, |
149 |
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to avoid "_diags" naming if no relation to pkg/diagnostics. |
150 |
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ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF |
151 |
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file and only call PLOT_FIELD_XYZ if debugMode=T. |
152 |
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remove few PLOT_FIELD_XY calls outside initialisation. |
153 |
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remove few unnecessary BARRIER. |
154 |
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o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling |
155 |
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of salt_plume package in Southern Ocean |
156 |
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o pkg/thsice: |
157 |
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- fix hOceMxL in overlap (needed for sea-ice advection); |
158 |
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update output of experiment global_ocean.cs32x15.icedyn. |
159 |
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o pkg/seaice: |
160 |
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- make the (placeholder-)tracer IceAge a little more meaningful |
161 |
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by avoiding ridging of age due to convergent ice flow |
162 |
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- add diagnostics for surface temperature, atmospheric and oceanic |
163 |
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heat flux, and atmospheric and oceanic ice growth |
164 |
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|
165 |
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checkpoint61p |
166 |
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o eesupp (global_max & global_sum): |
167 |
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- add one more element to buffer (start at index 0) for GL_MAX/SUM output; |
168 |
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- remove starting & endding barrier (no longer needed) |
169 |
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o pkg/mdsio, writelocal: |
170 |
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works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined |
171 |
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(remove the STOP): uses shared buffer IO to store data from all threads |
172 |
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and then let master-thread write nThreads tiles. |
173 |
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o pkg/mdsio (read/write field): |
174 |
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- tiled IO done in 1 piece (all levels at a time); |
175 |
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- new header file "MDSIO_BUFF_3D.h" with 3-D buffers. |
176 |
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- multi-threaded: allow to read/write local (non-shared) array |
177 |
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(was already working with singleCpuIO ; now works also without); |
178 |
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=> no longer needs barrier call after reading a file (added inside |
179 |
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mds_read/write field). |
180 |
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- move barrier calls outside gather/scatter_2d to mds_read/write_field |
181 |
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o pkg/obcs/exf |
182 |
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- exf_getffieldrec.F: add a few ". _d 0" and |
183 |
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add code to catch the case fldperiod = 0. |
184 |
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- obcs_precribe_read.F: change if statements so that they match |
185 |
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the variable type (_RL) |
186 |
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- add a separate exf_iprec_obcs to exf_set_obcs (by default equal to |
187 |
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exf_iprec) as part of namelist EXF_NML_01 |
188 |
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o pkg/mdsio: |
189 |
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- read/write tiled (local) files: read/write 1-level tile chunk at a time |
190 |
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(instead of segment of length sNx); expected to speed up tiled IO. |
191 |
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o pkg/exch2: |
192 |
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- take buffer copy from/to array out of S/R exch2_send/recv into new |
193 |
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S/R exch2_put/get ; Exch of local variable now works with MPI+MTH |
194 |
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(tested by removing commom block statement in SOLVE_FOR_PRESSURE.h). |
195 |
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- ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get) |
196 |
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- simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds |
197 |
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(which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by |
198 |
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including Topology header file (and common blocks). |
199 |
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- implement EXCH_IGNORE_CORNERS in scalar exchange (rx1); |
200 |
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remove 2nd exch call in exch2_s3d_rx (no longer needed). |
201 |
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- document S/R arg. list (+ update some comments) |
202 |
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o pkg/seaice: |
203 |
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- added SEAICE_CLIM_AIR code, which permits modulation of surface air |
204 |
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temperature and humidity over sea ice based on climatological values. |
205 |
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- clean up computation of Hibler+Bryan (1987) stress coupling for the case |
206 |
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of LSR (this change is expected to change the results slightly because now |
207 |
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it uses slightly difference moduli from the second last LSR solution, but |
208 |
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that is more consistent with the stress computations; this part of the code |
209 |
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is not tested in the verification experiments) |
210 |
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- fix diagnostics for flux of ice in case of B-grid |
211 |
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- turn strain rates eij and press into global fields within global |
212 |
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common block in SEAICE.h for more straighforward diagnostics |
213 |
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- fix diagnostics for principal stress components, press, zeta, eta |
214 |
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to give something meaning full |
215 |
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o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate |
216 |
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new output (all 4 tests) using default rotationPeriod. |
217 |
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o pkg KPP: |
218 |
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- add flag (LimitHblStable) to avoid limiting BL depth under stable conditions |
219 |
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- fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1 |
220 |
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and normal grid from 1 to Nr) |
221 |
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o Fix computations of L4rdt in mom_calc_visc.F |
222 |
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o eesupp: |
223 |
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new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg): |
224 |
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should be called before a "stop" if we know that all process are going |
225 |
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to stop; if one Proc does call this S/R, will hang in MPI_FINALISE. |
226 |
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|
227 |
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checkpoint61o |
228 |
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o pkg/exch2: change check_depths to issue just a warning (instead of error+stop) |
229 |
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o model/src/ini_curvilinear_grid.F: |
230 |
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compute angleSin/CosC when they are not read from a file |
231 |
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o pkg/seaice: |
232 |
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add pseudo time stepping for LSOR |
233 |
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o pkg/exch2: |
234 |
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temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW |
235 |
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o pkg/seaice: |
236 |
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Adding separate sea ice albedo, drag coefficients, and HO in Southern |
237 |
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Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h |
238 |
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o SingleCpuIO: |
239 |
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fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used. |
240 |
|
o pkg/seaice: |
241 |
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put exchanged variable in (local) common block for MPI+Multi-Threads |
242 |
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to work (necessary with exch1, and for now with exch2 too). |
243 |
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o verification: to get more experiments tested with mpi, mth and mpi+mth, |
244 |
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change tiling of: |
245 |
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aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15, |
246 |
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hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope |
247 |
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update output of exp: |
248 |
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exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5), |
249 |
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tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod) |
250 |
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+ ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU |
251 |
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(note: output.txt generated on faulks using only 1 tile) |
252 |
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o eesupp & mdsio (SingleCpuIO): |
253 |
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- remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time |
254 |
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parameter "W2_useE2ioLayOut" (read from file "data.exch2"). |
255 |
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Note: was not effective for globalFile & useSingleCpuIO=F; now fixed. |
256 |
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- move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc). |
257 |
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- fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same |
258 |
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gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array). |
259 |
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o pkg/exch2: |
260 |
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- new code to set-up W2-Exch2 topology (replace matlab-topology-generator): |
261 |
|
read parameter file "data.exch2" if it exists; otherwise try default regular |
262 |
|
cube without blank-tile; new header file "W2_EXCH2_SIZE.h"; |
263 |
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- update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible |
264 |
|
with new code (not to be used, just as a backup solution). |
265 |
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- add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2" |
266 |
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in utils/exch2/input. |
267 |
|
|
268 |
|
checkpoint61n |
269 |
|
o eesupp & mdsio (SingleCpuIO): |
270 |
|
- move mapping to global io-buffer inside gather_2d/scater_2d: this save |
271 |
|
memory (1 less 2D global RL array); skip 1 buffer copy; and only send/ |
272 |
|
receive real*4 array (instead of real*8) to read/write 32.bit files. |
273 |
|
(new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S |
274 |
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and remove new mapping S/R) |
275 |
|
o pkg/mdsio: in preparation for topology-generator within pkg/exch2: |
276 |
|
- Change declaration of SingleCpuIO buffer, reduced to only 1 dim.: |
277 |
|
xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h |
278 |
|
when using exch2. Add S/R to map global io-buffer to global model array. |
279 |
|
- uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt. |
280 |
|
|
281 |
|
checkpoint61m |
282 |
|
o write_utils : change WRITE_1D_R8 to WRITE_1D_RL |
283 |
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and add 3 other S/R for other types (R4,R8,RS). |
284 |
|
Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument. |
285 |
|
o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros): |
286 |
|
- ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ; |
287 |
|
- reduce number of macro definitions (keep only those which are used); |
288 |
|
can always call directly the corrresponding S/R if needed. |
289 |
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- everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix |
290 |
|
_R4/_R8 to _RS/_RL when applied to _RS/_RL variable. |
291 |
|
Fixed wrong type of arg in: |
292 |
|
atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F |
293 |
|
ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F |
294 |
|
To fix: global_sum of var in common block is wrong (multi-threaded) in: |
295 |
|
dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F |
296 |
|
To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops) |
297 |
|
o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd |
298 |
|
"nlfs" mpi test is going to stop when checking for unconnected tile egdes. |
299 |
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o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error |
300 |
|
o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile |
301 |
|
edges are closed (zero depth); might happen with "blank tiles"; |
302 |
|
for now, disabled if using OBCS. |
303 |
|
o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi": |
304 |
|
link *_mpi files from "MODS" dir) to return to a strait-forward behavior. |
305 |
|
o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D) |
306 |
|
to reduce length of 1.D array print in STDOUT. |
307 |
|
o adjustment.cs-32x32x1: changed to oceanic test with 1 continent |
308 |
|
+ use 48 tiles (16x8): this will allow to test "blank tiles". |
309 |
|
o start to test MPI + multi-threaded (change testreport to skip tests |
310 |
|
where number of tiles do not match). |
311 |
|
o genmake2: add option "-omp" to turn on Open-MP ; |
312 |
|
passed to testreport (if using -mth) ; merge few (*+mth) optfiles. |
313 |
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o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them) |
314 |
|
and keep the original tile numbering. Note: compatible with old |
315 |
|
W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files. |
316 |
|
|
317 |
|
checkpoint61l |
318 |
|
o Overlaps had been forgotten in calculating ijk keys : fixed |
319 |
|
o fix cyrus makedepend for gcc 4.4 |
320 |
|
o experiment fizhi-cs-aqualev20: |
321 |
|
switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE) |
322 |
|
and generate new output. Note: new output is much closer to the old |
323 |
|
one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from |
324 |
|
the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007. |
325 |
|
o pkg/fizhi: |
326 |
|
- change to avoid indices going deliberately over array-bounds |
327 |
|
- remove unnecessary MPI stuff |
328 |
|
- perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY" |
329 |
|
- new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE: |
330 |
|
does not go over array-bounds and therefore returns reliable output. |
331 |
|
- in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls: |
332 |
|
this S/R has 4 output arguments, which are used inside "get_alarm"; |
333 |
|
when it is called with the same variable "ndum" in place of several |
334 |
|
output arguments, this produces weird side effect inside "get_alarm" |
335 |
|
(e.g., datein=dates(n) is overwritten by timein=times(n) since both |
336 |
|
datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum" |
337 |
|
address) and produces error. |
338 |
|
o tools/gemake2: (March 27-29 2009) |
339 |
|
with option "-mpi": link *_mpi files from "MODS" dir (this is what |
340 |
|
testreport does). |
341 |
|
o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output |
342 |
|
o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F: |
343 |
|
update lab_sea.lsr & lab_sea.salt_plume results |
344 |
|
o pkg/seaice: |
345 |
|
Major overhaul of the LSOR solver: change discretization from original |
346 |
|
finite differences to finite volume. The old routine is still in the |
347 |
|
file seaice_lsr.F and can be turned on with the CPP-flag |
348 |
|
SEAICE_OLD_AND_BAD_DISCRETIZATION |
349 |
|
Along with this change, the discretization of the strain rates is changed. |
350 |
|
The same flag turns on the old discretization in seaice_calc_strainrates.F |
351 |
|
All verification experiments with seaice are affected (except for |
352 |
|
seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old |
353 |
|
results by setting the above flag. |
354 |
|
Further changes involve changes in defaults: |
355 |
|
- ALLOW_FLOODING is defined and turned on by default |
356 |
|
- SEAICEadvSnow = .true. is now the default |
357 |
|
- SEAICEadvSalt = .true. is now the default |
358 |
|
- SEAICEadvAge = .true. is now the default |
359 |
|
- SEAICE_clipVelocities = .false. is now the default |
360 |
|
(as per J. Zhang's recommendation) |
361 |
|
- B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE |
362 |
|
is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS |
363 |
|
- seaice_growth: replace computation of UG by a simple copy from wspeed |
364 |
|
|
365 |
|
checkpoint61k |
366 |
|
o pkg/seaice: a few bug fixes mostly concerning the metric terms: |
367 |
|
seaice_lsr: fixed a few metric terms, |
368 |
|
affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs |
369 |
|
add more debugging diagnostics |
370 |
|
seaice_evp: removed superfluous many metric terms of FV discretization |
371 |
|
of stress divergence |
372 |
|
affects lab_sea, lab_sea.hb87 |
373 |
|
seaice_ocean_stress: removed superfluous many metric terms of FV discretization |
374 |
|
of stress divergence for non-evp solver |
375 |
|
(this part is not tested anywhere) |
376 |
|
seaice_calc_strainrates: fixed a bug in no-slip boundary conditions, |
377 |
|
they were effectively only half slip |
378 |
|
affects lab_sea.hb87 |
379 |
|
updated all relevant verification experiments (except lab_sea//output_adm.txt |
380 |
|
which was left over, but fails at level 7 & 6) |
381 |
|
|
382 |
|
checkpoint61j |
383 |
|
o pkg/seaice: turn a few hard wired parameters into run time parameters |
384 |
|
o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model |
385 |
|
time in seconds as promised by the usints in seaice_monitor and exf_monitor |
386 |
|
o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids |
387 |
|
that are not cubed-sphere grids |
388 |
|
o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR |
389 |
|
o pkg/ctrl: |
390 |
|
fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low) |
391 |
|
o non-hydrostatic (calc_gw.F): |
392 |
|
fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec |
393 |
|
update output of exp. global_ocean.cs32x15.viscA4 |
394 |
|
o remove backward compatibility for thetaMin,phiMin |
395 |
|
(replaced by xgOrigin,ygOrigin on Jan 27, 2009) |
396 |
|
o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the |
397 |
|
interpolated wind field not only for curvilineargrid=.true., but also |
398 |
|
for a rotated grid (rotateGrid=.true.) |
399 |
|
o pkg/exf: add capability to bypass interpolation for runoff |
400 |
|
by setting yet another CPP-flag |
401 |
|
o eesupp/src, B-grid exchange: |
402 |
|
add simple (6 tiles, non MPI) CS exch + standard interface S/R. |
403 |
|
o autodiff |
404 |
|
new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV |
405 |
|
allows to switch to single-prec common blocks; |
406 |
|
corresponding switch occurs in tamc.h, integer isbyte |
407 |
|
TAF store directivs "byte" and "kind" seem equivalent; |
408 |
|
Most tamc.h have been updated correspondingly. |
409 |
|
|
410 |
|
checkpoint61i |
411 |
|
o autodiff: |
412 |
|
fix autodiff_sore/_restore indices for obcs |
413 |
|
(spotted by I. Hoteit, M. Mazloff) |
414 |
|
o pkg/autodiff, pkg/ctrl: |
415 |
|
Add flag to reduce all tapelev I/O to single-prec. |
416 |
|
In data.ctrl set |
417 |
|
doSinglePrecTapelev = .TRUE. |
418 |
|
o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2: |
419 |
|
check in hack for SX8 compiler (for dxV, dyU); remove it afterwards. |
420 |
|
o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for |
421 |
|
real fresh water flux (not yet) |
422 |
|
o pkg/mdsio & rw: |
423 |
|
- add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta) |
424 |
|
- add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX. |
425 |
|
o pkg/flt: |
426 |
|
- replace FLT_INIT by 3-steps standard initialization S/R: readparms, |
427 |
|
init_fixed & ini_varia. |
428 |
|
- clean-up & simplify linear interpolation S/R: |
429 |
|
move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid. |
430 |
|
- fix some indices (mainly vertical index) ; add IMPLICIT NONE. |
431 |
|
- more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R. |
432 |
|
- add vert. coordinate & horiz. indices to output files. |
433 |
|
- change vertical position in initial condition, from index to depth [m]. |
434 |
|
- store horizontal (decimal) indices i,j in common block (instead of coord. x,y) |
435 |
|
(easier to get to a curvilinear grid) ; delX,delY no longer used. |
436 |
|
o pkg/ggl90: a few modifications: |
437 |
|
- fix bottom boundary condition, and interpolation of KappaE |
438 |
|
near top and bottom |
439 |
|
- use same set of viscosity/diffusivity for TKE/momnetum/tracer |
440 |
|
- add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH) |
441 |
|
- add a few options for mixing-length upper limit (--> mxlMaxFlag) |
442 |
|
o rename thetaMin,phiMin -> xgOrigin,ygOrigin |
443 |
|
(maintain temporary backward compatibility, until next checkpoint) |
444 |
|
|
445 |
|
checkpoint61h |
446 |
|
o pkg/diagnostics with "periodic averaging diagnostics": |
447 |
|
fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output. |
448 |
|
o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82 |
449 |
|
o pkg/obcs: fix loop ranges for balancing code |
450 |
|
o pkg/flt: |
451 |
|
- improve criteria for finding which tile owns a float. |
452 |
|
- fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case. |
453 |
|
o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg |
454 |
|
aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling |
455 |
|
with ocean biogeo) |
456 |
|
o pkg/flt: |
457 |
|
- do some cleaning and fix the restart ; |
458 |
|
- add output.txt in flt_example/results to get this pkg tested. |
459 |
|
o genmake2: add an EXTENDED_SRC option and flag. |
460 |
|
for now, cannot be turned on on command line (only through genmake_local) |
461 |
|
o pkg/mdsio: read/write vector: |
462 |
|
- singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS |
463 |
|
- singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR |
464 |
|
& MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS. |
465 |
|
- affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO) |
466 |
|
(drop to 4 digits matching for grad). But this test does not look very |
467 |
|
reliable (was already failling on eddy, fc5, at 6.digits). Update output. |
468 |
|
|
469 |
|
checkpoint61g |
470 |
|
o pkg/flt: |
471 |
|
- move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name) |
472 |
|
+ make OPTIONS file more standard. |
473 |
|
- rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name) |
474 |
|
- fix _BYTESWAPIO CPP-Flag |
475 |
|
- standard reading of file-parameter "data.flt" |
476 |
|
- fix argument list of S/R FLT_RESTART |
477 |
|
still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F |
478 |
|
o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell |
479 |
|
o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to |
480 |
|
a still unfixed compiler/optimization bug |
481 |
|
|
482 |
|
checkpoint61f |
483 |
|
o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ; |
484 |
|
update results of global_ocean.cs32x15.icedyn test. |
485 |
|
o move getcon.F from model/src to pkg/fizhi. |
486 |
|
o pkg/exf: add parameter for extrapolation of temp up to the surface |
487 |
|
and option to prevent negative evap (in bulk_largeyeager04 only). |
488 |
|
o Prather Advection scheme: fix tracer conservation for divergent flow |
489 |
|
(e.g., when using NonLin Free-Surface). |
490 |
|
o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead |
491 |
|
o gmredi (Visbeck-variable-K): |
492 |
|
- add more parameters to Visbeck-variable-K. |
493 |
|
- use a 5 points average for dSigmaR in Visbeck-K calculation |
494 |
|
(more "homogenous": same stencil and same weights as in dSigmaH) |
495 |
|
- update output of ideal_2D_oce experiment. |
496 |
|
o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4 |
497 |
|
(#undef REAL4_IS_SLOW) |
498 |
|
- pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4 |
499 |
|
coordinate variable |
500 |
|
- pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables |
501 |
|
(surface forcing fields), removes some of the functionality |
502 |
|
- model/src/write_grid.F: write _RS variables as RS-netcdf variables |
503 |
|
- model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but |
504 |
|
probably not all: copy _RS surface flux fields to RL field before |
505 |
|
calling DIAGNOSTICS_FILL |
506 |
|
- model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into |
507 |
|
real*4 (CALL EXCH_*_RS) versions. |
508 |
|
- tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1 |
509 |
|
(generate new output). |
510 |
|
|
511 |
|
checkpoint61e |
512 |
|
o gmredi (Visbeck-variable-K): |
513 |
|
- fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h |
514 |
|
- change computation of Visbeck-K where Slope > Smax : |
515 |
|
now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct) |
516 |
|
previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output. |
517 |
|
o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic |
518 |
|
to be the same as with Z-coord. (i.e., m/s & no-units respectively). |
519 |
|
o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc) |
520 |
|
o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz |
521 |
|
does not become too large (to avoid precision problems in implicit-diffusion |
522 |
|
solver); update ideal_2D_oce output. |
523 |
|
o pkg ggl90: |
524 |
|
- in ggl90_cal.F: compute only one set of visc/diff, used to |
525 |
|
step forward TKE/T/S/momentum |
526 |
|
- default value of GGL90viscMax/GGL90diffMax larger and equal (to |
527 |
|
have Prandlt =1) |
528 |
|
o gmredi (fm07): |
529 |
|
- add lower limit on Transition layer thickness + lower limit on 1/lambda |
530 |
|
- allow to set few more params from data.gmredi |
531 |
|
o pkg ggl90: |
532 |
|
- add missing sqrt(2) factor in computation of mixing length |
533 |
|
scale in ggl90_calc.F |
534 |
|
(see Eq. (2.35) in Blanke and Delecluse, JPO, 1993) |
535 |
|
|
536 |
|
checkpoint61d |
537 |
|
o adjoint modifs |
538 |
|
- adapt to new field rhoInSitu |
539 |
|
- allow to revert from StoreDynVars2D, StoreDynVars3D |
540 |
|
to individual fields |
541 |
|
(switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D) |
542 |
|
o store 3-D (in-situ) density in commom block (DYNVARS.h) |
543 |
|
- save 1 rho computation. |
544 |
|
- no longer modify T & S inland when using down_slope pkg. |
545 |
|
o gad_som : allow to switch to SOM advection for T & S without corresponding |
546 |
|
pickup files (using new S/R: MDS_CHECK4FILE). |
547 |
|
o keep removing _BEGIN/_END_MASTER between MDSIO S/R call |
548 |
|
(for useSingleCpuIO to work in multi-threaded) |
549 |
|
o pkg/shelfice: |
550 |
|
- disentangle parameters: retire shelfIceFile in data/PARM05 and substitute |
551 |
|
with SHELFICEtopoFile in data.shelfice |
552 |
|
- move code for reading ice shelf topography and modifying hFacC into separate |
553 |
|
subroutines of the shelfice package |
554 |
|
- separate initialisation of "fixed" and "variable" variables |
555 |
|
- kTopC is not (yet) replaced by kSurfC, although this is possible |
556 |
|
o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s |
557 |
|
o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors) |
558 |
|
and rename: |
559 |
|
ini_phiref.F --> set_ref_state.F (+ set anelastic factors) |
560 |
|
ini_reference_state.F --> load_ref_files.F (- set anelastic factors) |
561 |
|
o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst) |
562 |
|
|
563 |
|
checkpoint61c |
564 |
|
o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid" |
565 |
|
to add mass source/sink of fluid in the interior (3-D generalisation |
566 |
|
of oceanic real-fresh water flux). |
567 |
|
o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max) |
568 |
|
o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before) |
569 |
|
o new pkg: down_slope |
570 |
|
density-driven downsloping flow parameterisation (Tellus, 1999, 412-430). |
571 |
|
- presently, modify T & S inland (dwnslp_calc_rho.F). |
572 |
|
can be avoided if rho was stored in common bloc and used in calc_phi_hyd. |
573 |
|
- implementation for ocean in P-coords not tested. |
574 |
|
- add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg. |
575 |
|
o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC) |
576 |
|
(to facilitate conversion of oceanic pkg to p-coordinate). |
577 |
|
o change FIND_RHO to FIND_RHO_2D : |
578 |
|
pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK. |
579 |
|
o new pkg: cheapaml |
580 |
|
|
581 |
|
checkpoint61b |
582 |
|
o exch2: |
583 |
|
change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS) |
584 |
|
- no longer depend on the order sequence (N,S,E,W). |
585 |
|
- 3rd exchange no longer needed (tested with 24 tiles). |
586 |
|
- same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff) |
587 |
|
- exch_UV_A-grid readily available (but not yet tested). |
588 |
|
comment out 3rd exch call and remove copy of V to U at SE & NE face-corners |
589 |
|
(both are no longer needed) in exch_uv: no effect in forward run; but |
590 |
|
get truncation error differences with adjoint exch. |
591 |
|
o exch2: |
592 |
|
- change index-bounds storage (moved from target to local tile, |
593 |
|
more intuitive this way) ; rename/remove some variables. |
594 |
|
- change utils/exch2/matlab-topology-generator & code_mods accordingly. |
595 |
|
|
596 |
|
checkpoint61a |
597 |
|
o exch2/matlab-topology-generator: |
598 |
|
fix bug in index bounds for N-S internal exchange (hard to tell if this |
599 |
|
had any effect on the solution). |
600 |
|
o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf |
601 |
|
is exceeded |
602 |
|
o testreport: modify syntax of awk, so that it works also with |
603 |
|
awk, and not only with nawk and gawk |
604 |
|
|
605 |
|
checkpoint61 |
606 |
|
o autodiff |
607 |
|
Change default for TAF usage by removing argument '-nonew_arg' |
608 |
|
This changes TAF subroutine argument list (ordering of active var.) |
609 |
|
Omission of this flag leads to incompatibility w.r.t. TAMC |
610 |
|
To restore TAMC-compatibility, need following modifs: |
611 |
|
* use adoptfile tools/adjoint_options/adjoint_tamc_compatibility |
612 |
|
* use CPP option #define AUTODIFF_TAMC_COMPATIBILITY |
613 |
|
Tested TAF version is 1.9.22 |
614 |
|
N.B.: exch2 hand-written adjoint code currently not TAMC compatible |
615 |
|
|
616 |
|
checkpoint60 |
617 |
|
--->>> This is the last checkpoint for which generating the adjoint |
618 |
|
--->>> is done via the TAMC-compatibility TAF-flag "-nonewarg" |
619 |
|
--->>> by default. |
620 |
|
--->>> Future checkpoints will ommit this flag by default. |
621 |
|
o pkg/generic_advdiff, os7mp: simplify and avoid division by zero. |
622 |
|
o pkg/grdchk: Add gradient check to etan0 perturbations. |
623 |
|
o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK). |
624 |
|
o pkg/autodiff: more flexibility in zeroadj. |
625 |
|
model/src: modifying do_oceanic_phys.F accordingly. |
626 |
|
o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation. |
627 |
|
o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option |
628 |
|
special setup of gmredi for which the adjoint is stable |
629 |
|
enough for parameter optimization. |
630 |
|
o bridging the gap between eddy stress and GM. |
631 |
|
-> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi) |
632 |
|
along with a change in CPP option (now ALLOW_EDDYPSI). |
633 |
|
-> when using GM w/ GM_AdvForm: |
634 |
|
The total eddy streamfunction (Psi = eddyPsi + K x Slope) |
635 |
|
is applied either in the tracer Eq. or in momentum Eq. |
636 |
|
depending on data.gmredi (intro. GM_InMomAsStress). |
637 |
|
-> ALLOW_EDDYPSI_CONTROL for estimation purpose. |
638 |
|
The key modifications are in model/src/taueddy_external_forcing.F |
639 |
|
pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F |
640 |
|
|
641 |
|
checkpoint59r |
642 |
|
o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array |
643 |
|
from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F); |
644 |
|
fix option to read coriolis(@ cell-corner) from files with CS-grid. |
645 |
|
o pkg/mnc: add some attributes to standard 1D-coordinate variables |
646 |
|
o pkg/diagnostics: enforce missing_value attribute for scalar variables at |
647 |
|
mass points, when using mnc for output |
648 |
|
- add runtime parameter (missing_value, missing_value_int) to override |
649 |
|
default (which is the value of getcon('UNDEF')) |
650 |
|
o pkg/mnc: prepare mnc for the actual use of missing values with the |
651 |
|
diagnostics package: small fix in mnc_cw_readwrite.template and more |
652 |
|
initialisation of never used fields |
653 |
|
- replace mnc_common.h and mnc_id_header.h with corresponding upper case |
654 |
|
versions |
655 |
|
o pkg/thsice/thsice_ini_vars.F added default initial values so that |
656 |
|
thermodynamics sea ice solver does not blow up when some initial fields |
657 |
|
are missing. |
658 |
|
o move from external_forcing_surf.F to ini_forcing.F |
659 |
|
the p-coord. hack consisting in using pLoad to set phi0surf ; |
660 |
|
update output of tutorial_global_oce_in_p (affected @ truncation level). |
661 |
|
o Freshen up a bit hs94.1x64x5, notably: |
662 |
|
remove rotationPeriod and tRef=5*0. (adjoint only), and add |
663 |
|
exactConserv=.TRUE. |
664 |
|
o pkg/generic_advdiff: |
665 |
|
change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only |
666 |
|
applies to files where Temperature & Salinity 2nd Order moments are used. |
667 |
|
o pkg/ptracers: add second-order moment advection schemes (80 and 81); |
668 |
|
this uses a dynamically allocated internal state data structure |
669 |
|
(#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) |
670 |
|
and requires a fortran 90 compiler |
671 |
|
|
672 |
|
checkpoint59q |
673 |
|
o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3) |
674 |
|
(from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977) |
675 |
|
o Refresh tutorial_global_oce_biogeo, notably: |
676 |
|
- change bathymetry (put back seamounts in ACC, use hFacs) |
677 |
|
- change EOS (POLY3 --> JMD95Z) |
678 |
|
- use Bryan-Lewis vertical diffusivity |
679 |
|
- use multidimensional advection |
680 |
|
- remove old virtual virtual in dic pkg, now done through ptracer pkg |
681 |
|
- change a couple of parameters in dic pkg |
682 |
|
o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F |
683 |
|
o pkg/obcs: change default to OBCSfixTopo = .true., |
684 |
|
- set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result |
685 |
|
- replace "debugMode" with "debugLevel .GE. debLevB" |
686 |
|
o implementation of TAF directives for gchem,cfc,dic |
687 |
|
o remove "exp5" (replaced by tutorial_deep_convection). |
688 |
|
o pkg/obcs: add code to fix topography gradients normal to open boundaries; |
689 |
|
this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms; |
690 |
|
the code can be turned on by setting OBCSfixTopo = .true. in data.obcs |
691 |
|
--> changes results in exp4, seaice_obcs |
692 |
|
o tutorial_deep_convection : |
693 |
|
update the set-up and increase resolution and domain size ; start |
694 |
|
from pseudo initial conditions = output at t=120mn in order to see |
695 |
|
something happening when running testreport. |
696 |
|
o pkg/seaice: add os7mp as an advection scheme |
697 |
|
add check for advection schemes |
698 |
|
add a flag for restoring T and S underneath sea ice |
699 |
|
o pkg/my82: add netcdf-support and diagnostics |
700 |
|
o thsice pkg: |
701 |
|
- Now hsMax limits snow height by turning it into ice following |
702 |
|
flooding scheme (and now conserving energy) |
703 |
|
- Slight rewriting of the formula in thsice_calc_thick.F |
704 |
|
- Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos |
705 |
|
--> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice |
706 |
|
|
707 |
|
checkpoint59p |
708 |
|
o gchem / dic / cfc : |
709 |
|
- add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h); |
710 |
|
- add new parameter files: "data.dic" & "data.cfc" ; |
711 |
|
- various re-arrangement in initialisation & header file ; |
712 |
|
- fix tutorial_global_oce_biogeo for multi-threaded test. |
713 |
|
o pkg/dic: test for "pickup_dic" file when restarting ; |
714 |
|
if no pickup-file, can restart with a re-initialised pH (same as it did |
715 |
|
before) providing pickupStrictlyMatch is set to False. |
716 |
|
o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP |
717 |
|
+ fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP |
718 |
|
o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2 |
719 |
|
and staggerTimeStep is off (needed for stability of Internal-wave dynamics). |
720 |
|
o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax, |
721 |
|
& lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers |
722 |
|
(note: not clear to me what lambdaTr1ClimRelax is still used for ...) |
723 |
|
o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which |
724 |
|
scheme to use for vorticty-term ; |
725 |
|
- compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F |
726 |
|
(with default selectVortScheme, return to original discretisation) |
727 |
|
- remove weird combination (e.g.: upwindVorticity & highOrderVorticity) |
728 |
|
o pkg/seaice: add a line to the summary to indicate grid type (B/C) |
729 |
|
o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the |
730 |
|
bottom ; only used with variable horizontal viscosity and non-hydrostatic. |
731 |
|
also fix diagnostics VISCAHW & VISCA4W. |
732 |
|
|
733 |
|
checkpoint59o |
734 |
|
o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran). |
735 |
|
o change the loop ordering in most gad_*_adv_x.F to improve vectorization: |
736 |
|
move a few statemens out the main loop into separate loops |
737 |
|
o pkg/shelfice: |
738 |
|
- sort out freshwater flux; convert freshwater fluxes to mass fluxes |
739 |
|
(kg/m^2/s), does not break tests, because in verification/isomip, |
740 |
|
rhoConstFresh=rhoConst (by accident) |
741 |
|
- rearrange computation of tLoc, sLoc, pLoc to make code more efficient |
742 |
|
- move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into |
743 |
|
new file model/src/seawater.F, so that they are available for all pkgs. |
744 |
|
- convert potential temperature into in-situ temperature. This changes the |
745 |
|
isomip tests => update tests |
746 |
|
o add a flag writePickupAtEnd (default=true) to be able to suppress |
747 |
|
writing a pickup at the last timestep |
748 |
|
o tools/mpack-1.6 : |
749 |
|
- disable automake (not working) and autoconf (not needed). |
750 |
|
- update to version 1.6.4 which fix MD5 code on some 64 bits platforms |
751 |
|
also cleaner with much less compilation warnings. |
752 |
|
o pkg/profiles: |
753 |
|
rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg |
754 |
|
(for "less than 32 characters name" compiler requirement) |
755 |
|
o pkg/obcs and pkg/exf: added capability to specify seaice open boundary |
756 |
|
conditions that have a different sampling frequency than S/T/U/V obcs |
757 |
|
o pkg/diagnostics (stats-diags): |
758 |
|
- fix global Min/Max in case 1 processor get only empty tiles |
759 |
|
o genmake2: replace (4 times) |
760 |
|
make genmake_tc_1.o >> genmake_warnings 2>&1 |
761 |
|
with |
762 |
|
COMM="$CC $CFLAGS -c genmake_tc_1.c" |
763 |
|
echo $COMM >> genmake_warnings |
764 |
|
$COMM >> genmake_warnings 2>&1 |
765 |
|
to make genmake2 always see the value of CC as specified in the optfile. |
766 |
|
o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid. |
767 |
|
- add diagnostics for 1srt & 2nd Order moments and sub-grid variance. |
768 |
|
- modify verification advect_cs test to test SOM-advection on CS-grid. |
769 |
|
o pkg/ctrl: |
770 |
|
- Rewrite of ctrl_map_ini_ecco.F, |
771 |
|
introducing a generic routine (ctrl_map_ini_gen.F). |
772 |
|
- Modification of ctrl_bound/adctrl_bound handling control vector bounds. |
773 |
|
|
774 |
|
checkpoint59n |
775 |
|
o pkg/diagnostics: for large number of diagnostics, store diagnostic mate |
776 |
|
number in dedicate array "hdiag": |
777 |
|
- new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST |
778 |
|
with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST. |
779 |
|
- many small changes (integer format) for large number of diagnostics |
780 |
|
- start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with |
781 |
|
a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23. |
782 |
|
o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For |
783 |
|
usingSphericalGrid, this allows to define the rotated grid coordinates |
784 |
|
via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the |
785 |
|
geographical coordinates according to the inverse of the rotation defined |
786 |
|
by the Euler angles, so that Coriolis parameter and online-interpolation by |
787 |
|
exf works with the geographical coordinates on XC/YC/XG/YG. |
788 |
|
Naturally, this feature does not work with all packages, so some |
789 |
|
combinations are prohibited in config_summary (flt, flt_zonal, ecco, |
790 |
|
profiles), because there the coordinates are assumed to be regular |
791 |
|
spherical grid coordinates. |
792 |
|
o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc: |
793 |
|
- introduce isopycnal diffusion coefficient control. |
794 |
|
o tools/adjoint_options: |
795 |
|
- additional control vector components. |
796 |
|
o pkg/mnc: have mnc create marginally meaning full coordinate variables |
797 |
|
(that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 |
798 |
|
o pkg/mypackage: |
799 |
|
- add example of read/write pickup for state-var ; |
800 |
|
- add entry points to the main code for state-vars diags & write-pickup. |
801 |
|
o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year |
802 |
|
transitions for useExfYearlyFields |
803 |
|
- add new subroutine that determines the file to read from for |
804 |
|
use*YearlyFields = .TRUE. and .FALSE. |
805 |
|
- add a verification experiment to global_with_exf that tests |
806 |
|
useExfYearlyFields with USE_EXF_INTERPOLATION defined |
807 |
|
o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in |
808 |
|
analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new |
809 |
|
subroutines (which could be generated from a template, because they are |
810 |
|
almost identical), for now they are included in obcs_prescribe_read.F for |
811 |
|
simplicity |
812 |
|
o pkg/exf: |
813 |
|
- add a little more diagnostic to exf_interp_read (in analogy to |
814 |
|
mds_read_field, can be turned off with debugLevel < debugLevA=1) |
815 |
|
- improve vectorizability of exf_interp for TARGET_NEC_SX, makes code |
816 |
|
ugly but fast by unrolling short inner loops, inserting a unroll=8 |
817 |
|
directive in routine lagran, and splitting a loop and making do while the |
818 |
|
outermost loop (the latter requires the intoduction of index arrays) |
819 |
|
o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice |
820 |
|
o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver |
821 |
|
http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html |
822 |
|
o verification/seaice_obcs: updated for restart test and latest options |
823 |
|
o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different |
824 |
|
ice rheology (so-called truncated ellipse, that gets rid of tensile stress); |
825 |
|
for now this is only available for the C-grid code and also within |
826 |
|
#ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code |
827 |
|
|
828 |
|
checkpoint59m |
829 |
|
o pkg/seaice: use different time constant for melting (SEAICE_gamma_t) |
830 |
|
and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature |
831 |
|
o gad_som : fix flux output (& diagnostics) to have same units as other |
832 |
|
advection scheme fluxes (was previously multiplied by deltaT). |
833 |
|
o added verification/seaice_obcs both to test seaice open boundaries |
834 |
|
and to provide an example matlab scrpt for generating them |
835 |
|
o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume |
836 |
|
o pkg/salt_plume: clean up salt_plume_frac.F to |
837 |
|
remove redundancy in PlumeMethod 1 and 4 |
838 |
|
o pkg/kpp: added saltplume diagnostics |
839 |
|
o pkg/obcs and pkg/seaice: |
840 |
|
- do not set uice and vice to zero when OB*icefile are unspecified |
841 |
|
- OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default |
842 |
|
- moved seaice tracer obcs after call to seaice_growth |
843 |
|
o pkg/salt_plume: added various options for salt plume depth |
844 |
|
criterion and for vertical distribution of the salt |
845 |
|
|
846 |
|
checkpoint59l |
847 |
|
o pkg/ptracers: new version of ptracers pickup: |
848 |
|
read meta file and write only fields which are needed to restart. |
849 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
850 |
|
o pkg/seaice: |
851 |
|
- add timescale for melting due to warm mixed layer as a means of |
852 |
|
setting SEAICE_availHeatFrac more conveniently |
853 |
|
- add a CPP-flag/runtime parameter check for flooding algorithm |
854 |
|
- reformulated availHeat in seaice_growth.F to be independent of AREA |
855 |
|
o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent |
856 |
|
unit changes |
857 |
|
o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint |
858 |
|
o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC |
859 |
|
SX vector computer. |
860 |
|
o pkg/seaice: |
861 |
|
- removed SEAICE_FFIELDS.h and seaice_get_forcing.F |
862 |
|
seaice forcing fields can now be read only through pkg/exf |
863 |
|
- removed some unused halos |
864 |
|
o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP |
865 |
|
o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL |
866 |
|
or U/VICE from U/VWIND before computing U/VSTRESS |
867 |
|
|
868 |
|
checkpoint59k |
869 |
|
o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between |
870 |
|
dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results. |
871 |
|
o fix un-initialised variable problem (in mom_vecinv & shap_filt): |
872 |
|
all experiments pass when compile with un-initialised var. checking option. |
873 |
|
o added pkg/salt_plume |
874 |
|
o script to test restart (for now, in MITgcm_contrib/jmc_script) |
875 |
|
o pkg/seaice: new read/write pickup version. |
876 |
|
read meta file and write only fields which are needed to restart. |
877 |
|
( same logic as main pickup file ; also using pickupStrictlyMatch ) |
878 |
|
o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates) |
879 |
|
o lab_sea.hb87: modify the domain & update output.hb87.txt : |
880 |
|
lat-long grid & no-slip BC in seaice-dynamics produce different sigma12 |
881 |
|
at j=1 & j=Ny+1 : this case is not treated correctly in the restart |
882 |
|
process. Fixed here by closing the domain at the Northern boundary. |
883 |
|
o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD. |
884 |
|
o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing |
885 |
|
a set of consecutive levels in/from a 3-D array. |
886 |
|
o pkg/ptracers: |
887 |
|
use a 2 characters string ioLabel to identify tracer (if more than 99 tracers). |
888 |
|
to-do: fix pkg/diagnostics when large number of diagnostics are defined. |
889 |
|
|
890 |
|
checkpoint59j |
891 |
|
o in pkgs: dic, obcs, offline, rbcs: |
892 |
|
standard way to compute coeff. for time interpolation between 2 time reccords |
893 |
|
which retains full precision (& make results less dependent on compiler). |
894 |
|
update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo. |
895 |
|
o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those |
896 |
|
packages instead of reading ice cover and wind speed separately |
897 |
|
o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h |
898 |
|
(keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad |
899 |
|
to allow to compile customized code before the update) |
900 |
|
o cleaning-up: |
901 |
|
- fix CPP instruction syntax in pkg/obcs |
902 |
|
- replace (some) call to MDSIO S/R with call to RW interface S/R ; and |
903 |
|
add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio) |
904 |
|
- fix some threads issue in IO parts. |
905 |
|
o pkg/dic: |
906 |
|
- add tons of "_d 0" (--> much better testreports !) |
907 |
|
and then update outputs of tutorial_global_oce_biogeo |
908 |
|
o pkg/mom_fluxform: |
909 |
|
add a special version of momentum advection intended to conserve momentum |
910 |
|
next to a bathymetry step or a coastline edge. (default = off = #undef) |
911 |
|
o new read/write pickup version: |
912 |
|
- for now, only implemented for main (mdsio) pickup file. |
913 |
|
- write out only what is needed to restart; merge pickup_nh , pickup_ph |
914 |
|
and main pickup together. |
915 |
|
- read meta file; read only what is needed to restart; stop if a field |
916 |
|
is missing (if pickupStrictlyMatch=T, = the default) or try to restart |
917 |
|
if it make sense (even if the restart is not perfect). |
918 |
|
- if no meta file, assume that pickup to read corresponds exactly to |
919 |
|
a pickup that would currently be written. |
920 |
|
- read pickup written in the old format (until checkpoint59i) if it |
921 |
|
recognizes an old meta file (no field-list). |
922 |
|
- add a meta file in exp. which starts from a pickup: 2 cases: |
923 |
|
a) minimal meta file (with just file precision) + pickupStrictlyMatch=F |
924 |
|
e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta |
925 |
|
b) a meta file describing the content of the associated pickup file |
926 |
|
e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta |
927 |
|
o pkg/mdsio & pkg/rw: |
928 |
|
- new routine to read a meta file ; new set of routine to read |
929 |
|
Multiple-fields file (with meta file). |
930 |
|
o added open boundary conditions capability for seaice |
931 |
|
HSNOW, HSALT, UICE, and VICE |
932 |
|
|
933 |
|
checkpoint59i |
934 |
|
o adjoint: |
935 |
|
* fix multiDimAdvection adjoint |
936 |
|
(partial recomputation problem by TAF for fVerT(:,:,kDown) |
937 |
|
and comlev1 size definition (maxpass vs. max. number of tracers) |
938 |
|
* verification/global_ocean.90x45x15 adjoint now tests |
939 |
|
NLFS and multiDimAdvection using DST3 (=30) |
940 |
|
* verification/lab_sea now tests multiDimAdvection using DST3 (=30) |
941 |
|
o pkg/kpp: add "_d 0" to real constant (if missing); |
942 |
|
update output of exp: natl_box (10.digits); vermix (std, 7.digits) |
943 |
|
and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits). |
944 |
|
o prepare for "clever pickup" implementation: add new header file "RESTART.h" |
945 |
|
for internal parameters related to restart process (formerly from PARAMS.h) |
946 |
|
and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2. |
947 |
|
o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed |
948 |
|
as argument. (only atm2d & obcs write_pickup have not yet been updated) |
949 |
|
o pkg/monitor: |
950 |
|
- use GLOBAL_SUM_TILE instead of _GLOBAL_SUM |
951 |
|
- fix mon_stats_rs (statistics over the full domain, even where field is zero) |
952 |
|
- account for deep Atmosphere factor and density factor (anelastic) |
953 |
|
o added open boundary conditions capability for seaice HEFF and AREA |
954 |
|
o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989) |
955 |
|
thermodynamics |
956 |
|
- requires a little reorganization, which affects the testreport results |
957 |
|
of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment, |
958 |
|
so that now the conservative form is tested |
959 |
|
- add a few comments |
960 |
|
o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code* |
961 |
|
o add a little bit of code to gad_os7mp_adv_?.F to help vectorization |
962 |
|
o add new diagnostics to seaice: advective, diffusive fluxes (only for |
963 |
|
multidim-advection, for scheme 2 they are not filled) and transports, |
964 |
|
thermodynamic growth rates |
965 |
|
o change units of EmPmR (inside the code, + within coupling interface) |
966 |
|
from m/s to kg/m2/s (mass flux) but leave input file unchanged. |
967 |
|
Affects results @ truncation level (cg2d match) and update output of |
968 |
|
experiments: lab_sea(6), global_ocean.90x40x15(10), |
969 |
|
global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11) |
970 |
|
+ adjoint results: global_ocean_ebm(11) and lab_sea (12). |
971 |
|
Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T). |
972 |
|
Next: will retire convertEmP2rUnit (simply using mass2rUnit instead). |
973 |
|
|
974 |
|
checkpoint59h |
975 |
|
o pkg/exf: |
976 |
|
- improve vectorization by moving if-statement out of loops in |
977 |
|
exf_mapfields, exf_radiation |
978 |
|
- exf_bulkformulae.F: introduce 2D fields and vectorize code |
979 |
|
o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package |
980 |
|
o testreport: |
981 |
|
- allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE |
982 |
|
monitor & update offline_exf_seaice exp. output. |
983 |
|
- AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost) |
984 |
o pkg/seaice: |
o pkg/seaice: |
985 |
- bug fix in the evp solver: boundary conditions were affected be |
- bug fix in the evp solver: boundary conditions were affected be |
986 |
masking of zMax/zMin (changes results) |
masking of zMax/zMin (changes results) |
1278 |
ATMOSPHERIC_LOADING is #define). |
ATMOSPHERIC_LOADING is #define). |
1279 |
o pkg/kpp: replaced _KPP_RL with _RL |
o pkg/kpp: replaced _KPP_RL with _RL |
1280 |
o bug fixes for vertical diffusivity computations when both KPP and |
o bug fixes for vertical diffusivity computations when both KPP and |
1281 |
3D diffusivity arrays are used. |
3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F |
1282 |
|
are no longer updating the vertical diffusivity array |
1283 |
|
(passed as argument) but are (re-) setting those arrays. |
1284 |
o pkg/seaice: fix bug in evp solver, while doing that |
o pkg/seaice: fix bug in evp solver, while doing that |
1285 |
- change (improve?) discretization of stress computations for both |
- change (improve?) discretization of stress computations for both |
1286 |
cgrid-lsr and evp solver |
cgrid-lsr and evp solver |
2762 |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
2763 |
- these scheme operate in a similar manner as KPP (without ghat, of |
- these scheme operate in a similar manner as KPP (without ghat, of |
2764 |
course), however there is only one diffusivity that is used for both |
course), however there is only one diffusivity that is used for both |
2765 |
temperature and salinity (and passive tracers)ç |
temperature and salinity (and passive tracers) |
2766 |
o add offline package |
o add offline package |
2767 |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
2768 |
provided by Stephanie Dutkiewicz |
provided by Stephanie Dutkiewicz |