4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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|
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checkpoint64p (2013/10/20) |
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o pkg/autodiff: |
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- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
10 |
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criteria, return to simple (default) tape IO format. |
11 |
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o pkg/mdsio (+ eesupp/src): |
12 |
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- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
13 |
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previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
14 |
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- fix globalFile and singleCpuIO options using simpler global mapping. |
15 |
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- new pairs of scatter/gather vector S/R (one for each type, generated from |
16 |
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template) corresponding to simpler global mapping. |
17 |
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- adread_write.F: switch to new S/R (but leave old calls commented) and write |
18 |
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to globalFile when parameter globalFiles is set to True. |
19 |
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- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
20 |
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o pkg/autodiff: |
21 |
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- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
22 |
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with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
23 |
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missing, just add a STOP if array type do not match. |
24 |
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o pkg/exf: |
25 |
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- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
26 |
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rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
27 |
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and rename array obsSIce to exf_iceFraction. |
28 |
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o tutorial_deep_convection: |
29 |
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- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
30 |
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for now all in this exp. code dir. |
31 |
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- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
32 |
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testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
33 |
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o eesupp/src: |
34 |
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- added SINGLE_DISK_IO option because reading of parameter files on |
35 |
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very large number of processors did not work with existing set-up |
36 |
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|
37 |
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checkpoint64o (2013/09/25) |
38 |
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o pkg/atm_phys & atm_compon_interf: |
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- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
40 |
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o tools/build_options: |
41 |
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- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
42 |
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& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
43 |
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remove CPP setting (was identical to genmake2 default). |
44 |
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o pkg/gmredi & model/src: Some updating and work done on the residual model. |
45 |
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- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
46 |
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- fixed up the calculation of the eddy stress and how it is added to the |
47 |
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external forcing via taueddy_external_forcing.F |
48 |
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- at the moment, it is very experimental and only works with the variable eddy |
49 |
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diffusivity calculated in gmredi_k3d.F |
50 |
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o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
51 |
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lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
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o testreport (& tools/do_tst_2+2): |
53 |
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- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
54 |
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o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
55 |
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- remove CPP='cpp -traditional -P' (this is genmake2 default) |
56 |
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- add switch (for big setups) to use 'medium' memory-model (but leave it |
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commented out for now). Note: needed with FC 19 to compile big setups. |
58 |
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o pkg/atm_compon_interf: |
59 |
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- regroup per field origin (model & pkgs) the coupling storage routines |
60 |
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(which accumalate in time each coupling field) |
61 |
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- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
62 |
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update accordingly + simplify aim_do_physics.F |
63 |
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|
64 |
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checkpoint64n (2013/08/26) |
65 |
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o pkg/bbl: |
66 |
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- update formulation to reduce dispersion of tracer properties in bbl |
67 |
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- replaced horizontal and vertical transport parameters with velocities |
68 |
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- changes results for verification/global_with_exf.yearly |
69 |
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o verification/halfpipe_streamice: |
70 |
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- change to matrix construction; update both Fwd & AD output. |
71 |
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o verification/tutorial_tracer_adjsens: |
72 |
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- OpenAD test: switch to vector-invariant momentum since fluxform with |
73 |
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rStar causes problems with OpenAD; update output. |
74 |
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o tools: |
75 |
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- genmake2: define a common prefix for all temp-file names ; move them |
76 |
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to local /tmp disk (but would be easy to move them back); |
77 |
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- xmakedepend: apply the same switch for temp-files. |
78 |
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o pkg/offline: |
79 |
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- changes for use with rStar (NLFS): assume that we continue to provide |
80 |
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UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
81 |
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output files) and apply r* scaling at each time-step (function of the time |
82 |
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varying Eta field); use normal pickup files (needed for restart with NLFS). |
83 |
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o adjoint with OpenAD: |
84 |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
85 |
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package openad. This package has to be compiled for all runs with OpenAD |
86 |
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instead of specifying code_oad_all as a modification directory. |
87 |
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- link the fortran templates from tools/OAD_support to the build directory |
88 |
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for preprocessing to avoid conflicts between different setups compiled |
89 |
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simultaneously and simplify cleanup. |
90 |
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o pkg/exf: |
91 |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
92 |
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main model or other pkgs are exchanged in EXF_MAPFIELDS). |
93 |
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o model/src: |
94 |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
95 |
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(similar to do_fields_blocking_exchanges.F). |
96 |
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o tools/genmake2: |
97 |
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- remove TAF output src code just before calling staf (when not doing a fresh |
98 |
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built, will stop if things go wrong with staf). |
99 |
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- fix target "adobj" (left from TAF version-2 transition) |
100 |
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o pkg/diagnostics: |
101 |
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- add a parameter to track the status of pkg/diagnostics activation; |
102 |
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this replace/extend the use of logical param "settingDiags" (to check |
103 |
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when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
104 |
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New S/R to print error message and stop when pkgStatus is not right. |
105 |
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- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
106 |
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|
107 |
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checkpoint64m (2013/08/13) |
108 |
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o model/inc: |
109 |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
110 |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
111 |
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o pkg/kpp & aim_v23: |
112 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
113 |
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o pkg/seaice: |
114 |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
115 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
116 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
117 |
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o eesupp/src: |
118 |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
119 |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
120 |
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o switch to TAF version-2: |
121 |
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- add flow directives to "freeze" naming convention for ad-routines that |
122 |
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are used in I/O routines of adjoint state and associated common blocks |
123 |
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that are used in adcommon.h (backward compatible with version-1) |
124 |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
125 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
126 |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
127 |
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out except for diva). |
128 |
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- the major change with TAF version-2 is that both the differentiated |
129 |
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routines and the forward routines (new) are returned as part of the TAF |
130 |
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output source code. Update genmake2 accordingly. |
131 |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
132 |
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with version-2 when compared to TLM or FWD gradient); other experiments |
133 |
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output show minor changes (machine truncation level); update the few AD & |
134 |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
135 |
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|
136 |
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checkpoint64l (2013/08/05) |
137 |
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o model/src: |
138 |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
139 |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
140 |
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when using TAF but only if using OpenAD. |
141 |
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o pkg/mom_common+fluxform+vecinv: |
142 |
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- always set horiz. viscosity arrays to background value before calling |
143 |
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MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
144 |
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only when using variable horiz. viscosity (useVariableVisc=T); |
145 |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
146 |
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o pkg/mom_common: variable horiz. viscosity in NH code |
147 |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
148 |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
149 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
150 |
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useBiharmonicVisc & useVariableVisc. |
151 |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
152 |
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in calc_gw.F, version 1.27, 2006/06/20): |
153 |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
154 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
155 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
156 |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
157 |
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any type of variable viscosity, e.g., viscAh/4Grid) |
158 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
159 |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
160 |
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horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
161 |
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default viscAh,viscA4 is zero). |
162 |
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o model/src: |
163 |
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- extend length of drC & recip_drC from Nr to Nr+1. |
164 |
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o Divided Adjoint (DIVA) with MPI: |
165 |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
166 |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
167 |
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and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
168 |
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|
169 |
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checkpoint64k (2013/07/23) |
170 |
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o tools/OAD_support: |
171 |
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- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
172 |
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and remove it from genmake2. |
173 |
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o tools/build_options: |
174 |
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- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
175 |
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MPI_HEADER_FILES list (let genmake2 find the missing headers) |
176 |
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o verification/halfpipe_streamice: |
177 |
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- change to driving stress formulation; update both Fwd & AD output. |
178 |
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o tools/genmake2 and Divided Adjoint with MPI: |
179 |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
180 |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
181 |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
182 |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
183 |
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Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
184 |
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- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
185 |
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o testreport: |
186 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
187 |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
188 |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
189 |
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o verification/lab_sea (AD test): |
190 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
191 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
192 |
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o pkg atm_ & ocn_compon_interf: |
193 |
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- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
194 |
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staggerTimeStep implementation) and disable (retired) corresponding |
195 |
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parameter. |
196 |
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o pkg/offline: |
197 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
198 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
199 |
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and stop if loading a file that is not used; |
200 |
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- enable to calculate GMRedi tensor, KPP mixing and convective index |
201 |
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when the corresponding file(s) is/are not specified (but pkg is used). |
202 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
203 |
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for monitoring CFL numbers and checking offline fields. |
204 |
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o OpenAD: |
205 |
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- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
206 |
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smaller standard output) and generate new (smaller) output (on baudelaire |
207 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
208 |
|
o model/src: |
209 |
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- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
210 |
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(where external_forcing_adjust was called) and change list of arguments; |
211 |
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- merge external_forcing_adjust.F into external_forcing_surf.F |
212 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
213 |
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which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
214 |
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previously in file "balance_relax.F", now removed); remove corresponding |
215 |
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arrays in FFIELDS.h. |
216 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
217 |
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a hack for getting back surfaceForcingS (loaded from file) when using |
218 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
219 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
220 |
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(was getting only 11 digits for AD-grad, due to different truncation |
221 |
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error in AD code). |
222 |
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|
223 |
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checkpoint64j (2013/07/04) |
224 |
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o pkg/offline: |
225 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
226 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
227 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
228 |
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o pkg/exf ALLOW_RUNOFTEMP |
229 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
230 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
231 |
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- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
232 |
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o pkg/atm_phys: |
233 |
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- allows to add some damping on uVel,vVel (strength only function of k). |
234 |
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o verification, ad-tests: |
235 |
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- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
236 |
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global_ocean_ebm and offline_exf_seaice.thsice. |
237 |
|
o verification/halfpipe_streamice: |
238 |
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- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
239 |
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flux input boundary conditions to be ignored; a fix for this bug changed |
240 |
|
verification results for forward test. |
241 |
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- add adjoint test. |
242 |
|
o pkg/ptracers: |
243 |
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- allow to restart without SOM pickup (resetting SOM to zero). |
244 |
|
o pkg/gmredi: |
245 |
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- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
246 |
|
- It uses mixing length theory and suppression by steering level effects to |
247 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
248 |
|
to JPO, for more details). |
249 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
250 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
251 |
|
- New files added to pkg/gmredi: |
252 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
253 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
254 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
255 |
|
for use in gmredi_k3d |
256 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
257 |
|
the eddy diffusivity |
258 |
|
|
259 |
|
checkpoint64i (2013/06/18) |
260 |
|
o pkg/cheapaml: |
261 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
262 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
263 |
|
with pkg/cheapaml. |
264 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
265 |
|
simple cs.pcol to plot 2D fields on a map |
266 |
|
o pkg/streamice: |
267 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
268 |
|
sheets and ice streams |
269 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
270 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
271 |
|
ed that this will change) |
272 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
273 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
274 |
|
rectangular embayment |
275 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
276 |
|
- for questions, email dgoldber@mit.edu |
277 |
|
o pkg/thsice: |
278 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
279 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
280 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
281 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
282 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
283 |
|
o pkg/cfc: |
284 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
285 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
286 |
|
- change some hard-coded constant to run time parameter for reading and |
287 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
288 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
289 |
|
- put arguments in standard order: myTime, myIter, myThid |
290 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
291 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
292 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
293 |
|
- new routine to print summary of CFC params and check for consistency. |
294 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
295 |
|
similar to thsice_advdiff. |
296 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
297 |
|
o pkg/cfc: |
298 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
299 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
300 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
301 |
|
hemisphere value. |
302 |
|
o pkg/seaice: |
303 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
304 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
305 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
306 |
|
- requires an additional time level that is stored in the pickup |
307 |
|
- you can start with AB2 from a pickup without this time level with |
308 |
|
pickupStrictlyMatch = .false. |
309 |
|
|
310 |
|
checkpoint64h (2013/05/26) |
311 |
|
o pkg/cheapaml: |
312 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
313 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
314 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
315 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
316 |
|
(Note: was already the case for Tair,Qair advection); |
317 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
318 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
319 |
|
- fill in array "Qsw" (for short-wave heating); |
320 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
321 |
|
before any update (consistent with MITgcm state var diagnostics); |
322 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
323 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
324 |
|
o pkg/seaice: |
325 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
326 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
327 |
|
- allows to compile pkg/seaice without pkg/exf. |
328 |
|
o tools/OAD_support: |
329 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
330 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
331 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
332 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
333 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
334 |
|
o pkg/offline: |
335 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
336 |
|
(previously called from pkg/dic_surfforcing_init.F) |
337 |
|
o model/src: |
338 |
|
- re-order sequence of calls within packages_init_variables.F, using |
339 |
|
standard order, except for: |
340 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
341 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
342 |
|
o new pkg: atm_phys |
343 |
|
- add entry point and source code (previously in contrib |
344 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
345 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
346 |
|
- re-order sequence of calls within packages_readparms.F, |
347 |
|
packages_init_fixed.F and packages_write_pickup.F |
348 |
|
(but skip packages_init_variables.F because of TAF issues). |
349 |
|
- update contrib/*/atm_gray/ experiment. |
350 |
|
o pkg/seaice (ITD code): |
351 |
|
- simplify and fix the writing of pickup-files for ITD case |
352 |
|
o pkg/seaice (ITD code): |
353 |
|
- introduce floe size dependent lateral melt for ITD case; |
354 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
355 |
|
- update seaice_itd experiment main output. |
356 |
|
o pkg/thsice: |
357 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
358 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
359 |
|
changed accordingly pkg/atm2d. |
360 |
|
|
361 |
|
checkpoint64g (2013/05/01) |
362 |
|
o pkg/exf ALLOW_RUNOFTEMP |
363 |
|
- if defined, river and glacier runoff temperature can be read-in from |
364 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
365 |
|
o pkg/thsice (& pkg/bulk_force): |
366 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
367 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
368 |
|
- change computation domain to always be the interior (without overlap). |
369 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
370 |
|
o verification/tutorial_global_oce_biogeo: |
371 |
|
- add preliminary OpenAD setup (still has problems) |
372 |
|
o pkg/seaice: |
373 |
|
- turn some parameters for choosing the convergence criterion of |
374 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
375 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
376 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
377 |
|
the results of lab_sea/input because a division has been replaced by |
378 |
|
a multiplication with the reciprocal (sumNorm) |
379 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
380 |
|
convergence of solver (changes results, of course), and to test some |
381 |
|
new features |
382 |
|
o model/src: |
383 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
384 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
385 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
386 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
387 |
|
o pkg/shelfice: |
388 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
389 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
390 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
391 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
392 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
393 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
394 |
|
- update isomip experiment forward output (get machine truncation error |
395 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
396 |
|
o verification/offline_exf_seaice: |
397 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
398 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
399 |
|
SEAICE_growMeltByConv = .TRUE., |
400 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
401 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
402 |
|
o verification/global_ocean.cs32x15: |
403 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
404 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
405 |
|
o verification/offline_exf_seaice: |
406 |
|
- adjust list of tested variables (with testreport) and update |
407 |
|
standard test output with better slection of monitored fields. |
408 |
|
o pkg/cd_code: |
409 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
410 |
|
experiment lab_sea.hb87 |
411 |
|
o tools/genmake2: |
412 |
|
- change default makedepend from the system default to tools/xmakedepend: |
413 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
414 |
|
otherwise select the system default (if exist and pass the test) or |
415 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
416 |
|
o pkg/exf & pkg/thsice: |
417 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
418 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
419 |
|
1) Rain has same temp as Air. |
420 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
421 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
422 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
423 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
424 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
425 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
426 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
427 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
428 |
|
o pkg/thsice: |
429 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
430 |
|
implementation): move THSICE_AVE call after the advection (called directly |
431 |
|
from thsice_do_advect.F). |
432 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
433 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
434 |
|
multiDimAdvection=.FALSE., |
435 |
|
There is still an issue with this. |
436 |
|
o pkg/thsice: |
437 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
438 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
439 |
|
and offline_exf_seaice (main test). |
440 |
|
|
441 |
|
checkpoint64f (2013/03/31) |
442 |
|
o verification/OpenAD: |
443 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
444 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
445 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
446 |
|
o verification/tutorial_global_oce_biogeo: |
447 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
448 |
|
o verification/offline_exf_seaice: |
449 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
450 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
451 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
452 |
|
o pkg/seaice/seaice_evp.F: |
453 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
454 |
|
the turningAngle is non-zero) over open water to avoid stripes |
455 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
456 |
|
the verification experiment (because turningAngle=0 in that experiment), |
457 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
458 |
|
o verification, AD & TLM output: |
459 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
460 |
|
additions and multiplications which affect results at machine truncation |
461 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
462 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
463 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
464 |
|
digits of matching. |
465 |
|
o pkg/seaice: |
466 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
467 |
|
"zebra" method: split vector loop into two with step size 2; this |
468 |
|
solves a general convergence problem for the JFNK solver on a vector |
469 |
|
computer. It has the potential to even improve convergence for |
470 |
|
non-vector machines, but it does change the results so it is turned |
471 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
472 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
473 |
|
|
474 |
|
checkpoint64e (2013/03/05) |
475 |
|
o pkg/ecco and several verification experiments: |
476 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
477 |
|
from ecco package, and revert to unified routine in model/src/ |
478 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
479 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
480 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
481 |
|
o pkg/generic_advdiff: |
482 |
|
- implement compressible flow method for multi-dim advection (similar to |
483 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
484 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
485 |
|
vertical advection. |
486 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
487 |
|
to test compressible flow multi-dim advection. |
488 |
|
o pkg/generic_advdiff: |
489 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
490 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
491 |
|
o pkg/seaice: |
492 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
493 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
494 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
495 |
|
seaice_calc_strainrates.F; |
496 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
497 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
498 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
499 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
500 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
501 |
|
- new subroutines seaice_lsr_tridiagu/v |
502 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
503 |
|
additive Schwarz method, but not used for now. |
504 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
505 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
506 |
|
o OpenAD support |
507 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
508 |
|
OpenAD revolve loop replacement |
509 |
|
(new S/R main_do_loop.F) |
510 |
|
o model/src: |
511 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
512 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
513 |
|
ADAMS_BASHFORTH2. |
514 |
|
o pkg/cheapaml: |
515 |
|
- add new parameter (default=F, same as before) to disable full domain |
516 |
|
(including land) periodicity in X & Y dir. |
517 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
518 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
519 |
|
into single S/R CHEAPAML_TIMESTEP. |
520 |
|
|
521 |
|
checkpoint64d (2013/02/17) |
522 |
|
o pkg/monitor (angular momentum): |
523 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
524 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
525 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
526 |
|
each component (instead of from cell centered averaged) and use the 4 |
527 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
528 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
529 |
|
FreeSurf) if using vectorInvariant momentum. |
530 |
|
o model/src (horizontal grid): |
531 |
|
- move initialisation of all horizontal grid arrays to null value |
532 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
533 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
534 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
535 |
|
compute them in S/R CALC_GRID_ANGLES. |
536 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
537 |
|
SEAICE_JFNK_tolIter |
538 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
539 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
540 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
541 |
|
- extend loop range in seaice_calc_viscosity |
542 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
543 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
544 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
545 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
546 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
547 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
548 |
|
for output.dyn_jfnk.txt |
549 |
|
in seaice_fgmres.F (unrelated to RAS) |
550 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
551 |
|
efficient), but because this changes the results, turn it off by |
552 |
|
default |
553 |
|
- replace the save statement by local common blocks |
554 |
|
o utils/matlab: |
555 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
556 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
557 |
|
instead of local script "load_cs.m". |
558 |
|
o pkg/seaice: |
559 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
560 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
561 |
|
change the verification experiment, because of the particular domain |
562 |
|
decomposition |
563 |
|
o pkg/diagnostics: |
564 |
|
- change default missing_value from UNSET_RL to -999. |
565 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
566 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
567 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
568 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
569 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
570 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
571 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
572 |
|
- moved the search algorithm into a separate subroutine, that is kept |
573 |
|
within the same file for automatic inlining. |
574 |
|
- modified catching potential errors |
575 |
|
o pkg/ecco: |
576 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
577 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
578 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
579 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
580 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
581 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
582 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
583 |
|
o model/src: |
584 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
585 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
586 |
|
and cpl_aim+ocn. |
587 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
588 |
|
for fizhi-cs experiments reference output. |
589 |
|
o pkg/ctrl: |
590 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
591 |
|
ALLOW_GENTIM2D_CONTROL |
592 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
593 |
|
o verification/global_ocean.cs32x15: |
594 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
595 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
596 |
|
o pkg/ptracers: |
597 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
598 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
599 |
|
o pkg/thsice: |
600 |
|
- implement new sequence of calls for thsice+seaice: |
601 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
602 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
603 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
604 |
|
in CPP_OPTIONS.h) to recover old sequence; |
605 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
606 |
|
just before advection (instead of just after advection in old sequence); |
607 |
|
- update output of experiment offline_exf_seaice (standard test); |
608 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
609 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
610 |
|
o pkg/aim_v23: |
611 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
612 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
613 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
614 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
615 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
616 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
617 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
618 |
|
o pkg/thsice: |
619 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
620 |
|
where just seaice diffusion is used without seaice-dynamics. |
621 |
|
|
622 |
|
checkpoint64c (2013/01/18) |
623 |
|
o pkg/seaice: |
624 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
625 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
626 |
|
- add a line search option to the JFNK solver |
627 |
|
- move update of u/vIce and computation of initial residual into a separate |
628 |
|
routine (same file); makes the code a little easier to read (?) |
629 |
|
- the line search requires computation of the residual and for some reason |
630 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
631 |
|
without changing the results, so we move computation of the new residual |
632 |
|
also to the end of the Newton loop, even without the line search |
633 |
|
o pkg/mdsio: |
634 |
|
- write missing value (corresponding to undefined array value) to meta files; |
635 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
636 |
|
case of undefined missing value but it's current the default missing-value); |
637 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
638 |
|
o pkg/exf & thsice: |
639 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
640 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
641 |
|
o verification/cfc_example: |
642 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
643 |
|
illustrate how to use it). |
644 |
|
o verification/offline_exf_seaice: |
645 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
646 |
|
files to only one time-record. |
647 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
648 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
649 |
|
snapshot output; same mcPheePiston value as in thsice with |
650 |
|
surf-current=0.2m/s. |
651 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
652 |
|
initial conditions). |
653 |
|
o verification/cfc_example: |
654 |
|
- update file "data" with more standard choice (default rotationPeriod, |
655 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
656 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
657 |
|
o pkg/layers: |
658 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
659 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
660 |
|
o verification/offline_exf_seaice: |
661 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
662 |
|
anywhere else). |
663 |
|
o verification/offline_exf_seaice: |
664 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
665 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
666 |
|
o model/src: |
667 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
668 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
669 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
670 |
|
- In order to be compatible with the default EVP code, this requires changing |
671 |
|
the EVP code around a little; and because any small change immediately |
672 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
673 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
674 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
675 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
676 |
|
The adjoint test lab_sea.evp also needed to be updated. |
677 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
678 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
679 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
680 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
681 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
682 |
|
kept obscure, because I need to test it a little more. |
683 |
|
o pkg/cheapaml: |
684 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
685 |
|
o pkg/seaice: |
686 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
687 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
688 |
|
o model/src: |
689 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
690 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
691 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
692 |
|
o pkg/cheapaml: |
693 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
694 |
|
update output of experiment cheapAML_box. |
695 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
696 |
|
and set them only in one place (cheapaml_readparms.F). |
697 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
698 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
699 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
700 |
|
o model/src/the_main_loop.F: |
701 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
702 |
|
o pkg/seaice: |
703 |
|
- remove legacy branch code. |
704 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
705 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
706 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
707 |
|
SEAICE_CAP_HEFF). |
708 |
|
o pkg/cheapaml: |
709 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
710 |
|
to load new forcing fields. |
711 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
712 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
713 |
|
cheapAML_box, keep same output (small trucation error differences). |
714 |
|
o verification/offline_exf_seaice: |
715 |
|
- add thermodynamics only test. |
716 |
|
o verification/cheapAML_box: |
717 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
718 |
|
keep same output (same 14 digits for cg2d). |
719 |
|
- switch on "-r8" compiler option (some numerical values are missing |
720 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
721 |
|
|
722 |
|
checkpoint64b (2012/12/24) |
723 |
|
o pkg/cheapaml: |
724 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
725 |
|
- store tendency of advected variables into cheapaml pickup file |
726 |
|
and fix the AB-2 restart. |
727 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
728 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
729 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
730 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
731 |
|
- update results after change of experiment seaice. |
732 |
|
o pkg/seaice: |
733 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
734 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
735 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
736 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
737 |
|
o model/src: |
738 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
739 |
|
(in case of a poor convergence). |
740 |
|
o pkg/seaice/seaice_lsr.F |
741 |
|
- move calculation of matrix coefficients into new |
742 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
743 |
|
file; the main purpose of this change is to be able to reuse the code |
744 |
|
in S/R SEAICE_PRECONDITIONER |
745 |
|
- modify the computation of the residual so that the mass of sea-ice |
746 |
|
is not used twice; this simplifies the calculations, but since |
747 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
748 |
|
not tested in testreport---this does not affect the testreport results. |
749 |
|
o verification/seaice_obcs: |
750 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
751 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
752 |
|
o model/src: |
753 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
754 |
|
o pkg/seaice: |
755 |
|
- improve description of parameters in seaice_fgmres.F and start |
756 |
|
cleaning up the code |
757 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
758 |
|
second argument |
759 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
760 |
|
results of offline_exf_seaice.dyn_jfnk |
761 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
762 |
|
o pkg/aim_v23: |
763 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
764 |
|
o model/src + pkg/seaice: |
765 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
766 |
|
along X and Y lines, respectively for U and V component. |
767 |
|
Note: 1) MPI and cube-exchange not yet coded. |
768 |
|
2) probably not accurate for poorly conditioned / large size problem. |
769 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
770 |
|
default: not compiled and not used. |
771 |
|
o pkg/seaice: |
772 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
773 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
774 |
|
mpi_allreduce in seaice_fgmres.F |
775 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
776 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
777 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
778 |
|
o verification: |
779 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
780 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
781 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
782 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
783 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
784 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
785 |
|
o pkg/exf: |
786 |
|
- disable "sstExtrapol" when Nr=1 |
787 |
|
o verification: |
788 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
789 |
|
to test pkg/cheapaml. |
790 |
|
o pkg/aim_v23 & pkg/shap_filt: |
791 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
792 |
|
o pkg/seaice: |
793 |
|
- remove unused field pressPre from jfnk solver |
794 |
|
- rename two subroutines in seaice_preconditioner.F |
795 |
|
o eesupp/src: |
796 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
797 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
798 |
|
- remove wrong parts of the rhs and the lhs (were in there |
799 |
|
because I did not understand the concept of this preconditioner) |
800 |
|
- add an exchange between u- and v-sweep. This increases communication |
801 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
802 |
|
one would like the u- and v-sweep to be independent. So far within |
803 |
|
undocumented ifdefs |
804 |
|
- reorganize the extra computations for printing the residuals |
805 |
|
o tools/genmake2: |
806 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
807 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
808 |
|
|
809 |
|
checkpoint64a (2012/11/16) |
810 |
|
o pkg/autodiff: |
811 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
812 |
|
autodiff_readparms.F no longer depends on calling order (within |
813 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
814 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
815 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
816 |
|
o pkg/obcs: |
817 |
|
- adding tidal velocity forcing capability to obcs |
818 |
|
for usage example, see verification/seaice_obcs/input.tides |
819 |
|
o pkg/seaice: |
820 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
821 |
|
SEAICE_LSRrelaxU/V |
822 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
823 |
|
o pkg/aim_v23: |
824 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
825 |
|
o pkg/shap_filt: |
826 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
827 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
828 |
|
o model/src: |
829 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
830 |
|
time-constant addMass field from file (addMassFile); |
831 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
832 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
833 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
834 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
835 |
|
o pkg/seaice: |
836 |
|
- complete merge of ITD code into seaice_growth.F |
837 |
|
from MITgcm_contrib/torge/itd/code/ |
838 |
|
no verification so far, but Torge Martin tested |
839 |
|
"1-D test case and Beaufort set up; |
840 |
|
deliver okay results after 1 model year." |
841 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
842 |
|
- move computation of eta at Z-points into calc_viscosities |
843 |
|
+ introduce global field etaZ |
844 |
|
+ add different methods for computing etaZ, for now the old |
845 |
|
method (simple averages of eta to Z-points) is hardwired |
846 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
847 |
|
seaice_preconditioner |
848 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
849 |
|
- seaice_preconditioner: |
850 |
|
+ replace one remaining press by pressLoc (mistake) |
851 |
|
+ adjust printing of residuals |
852 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
853 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
854 |
|
seaice_init_fixed.F) |
855 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
856 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
857 |
|
interval to STDOUT |
858 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
859 |
|
some operations |
860 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
861 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
862 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
863 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
864 |
|
a serious convergence problem when open boundaries are involved |
865 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
866 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
867 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
868 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
869 |
|
o pkg/autodiff |
870 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
871 |
|
SEAICEuseDYNAMICSinAdMode |
872 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
873 |
|
o pkg/seaice |
874 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
875 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
876 |
|
The code implements concept laid out in Thorndike et al. (1975); |
877 |
|
code is enabled via CPP flag SEAICE_ITD |
878 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
879 |
|
code is not complete yet!! |
880 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
881 |
|
o verification (using seaice): |
882 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
883 |
|
global_ocean.cs32x15.seaice ; update results. |
884 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
885 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
886 |
|
offline_exf_seaice (previously compiling B-grid). |
887 |
|
o pkg/exf: |
888 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
889 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
890 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
891 |
|
o pkg/layers (adjust changes from Sept 19): |
892 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
893 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
894 |
|
o pkg/layers (adjust changes from Sept 19): |
895 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
896 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
897 |
|
- remove layers variables when corresponding CPP option is undef. |
898 |
|
o pkg/layers: |
899 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
900 |
|
velocity in layer) |
901 |
|
o pkg/seaice: |
902 |
|
- simplify (?) ocean-drag coefficent computations by using |
903 |
|
the same routine in all three solvers (saves some code lines) |
904 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
905 |
|
declare them locally in lsr.F (the only place where they are |
906 |
|
still used) |
907 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
908 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
909 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
910 |
|
and SEAICEuseJFNK=.true. A few things to note: |
911 |
|
- involves a FGMRES, that is parallel but very inefficient, |
912 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
913 |
|
orthogonalization method. Needs to be replaced. Original code |
914 |
|
from J.-F. Lemieux |
915 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
916 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
917 |
|
preconditioner. For the preconditioner, the default is set to 10. |
918 |
|
- Jacobian times vector is computed with finite differences |
919 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
920 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
921 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
922 |
|
does not need this regularization in the first place). Define |
923 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
924 |
|
o eesupp/src: |
925 |
|
- check in genmake2 that intrinsic S/R flush is available. |
926 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
927 |
|
- flush standard & error msg unit before MPI termination |
928 |
|
- if debugMode, flush IO unit after printing msg |
929 |
|
o pkg/ctrl: |
930 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
931 |
|
to ctrl_set_unpack_xyz. |
932 |
|
|
933 |
|
checkpoint64 (2012/10/09) |
934 |
|
o pkg/shelfice |
935 |
|
- in mom_fluxform.F, mom_vecinv.F: |
936 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
937 |
|
Bug fix KappaRU -> KappaRV |
938 |
|
does not change verification/isomip but may change other setups |
939 |
|
(presumably constant KappaRU=KappaRV) |
940 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
941 |
|
o pkg/obcs: |
942 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
943 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
944 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
945 |
|
o pkg/seaice: |
946 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
947 |
|
default is off for now. |
948 |
|
o pkg/obcs: |
949 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
950 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
951 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
952 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
953 |
|
o pkg/layers : |
954 |
|
- add diagnostics to pkg/layers |
955 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
956 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
957 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
958 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
959 |
|
o pkg/seaice/seaice_growth.F: |
960 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
961 |
o pkg/obcs: |
o pkg/obcs: |
962 |
- change default setting of OBCS_UVICE_OLD from defined to undef; |
- change default setting of OBCS_UVICE_OLD from defined to undef; |
963 |
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |