4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
6 |
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|
7 |
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o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
8 |
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lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
9 |
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o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
10 |
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- remove CPP='cpp -traditional -P' (this is genmake2 default) |
11 |
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- add switch (for big setups) to use 'medium' memory-model (but leave it |
12 |
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commented out for now). Note: needed with FC 19 to compile big setups. |
13 |
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o pkg/atm_compon_interf: |
14 |
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- regroup per field origin (model & pkgs) the coupling storage routines |
15 |
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(which accumalate in time each coupling field) |
16 |
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- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
17 |
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update accordingly + simplify aim_do_physics.F |
18 |
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|
19 |
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checkpoint64n (2013/08/26) |
20 |
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o pkg/bbl: |
21 |
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- update formulation to reduce dispersion of tracer properties in bbl |
22 |
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- replaced horizontal and vertical transport parameters with velocities |
23 |
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- changes results for verification/global_with_exf.yearly |
24 |
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o verification/halfpipe_streamice: |
25 |
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- change to matrix construction; update both Fwd & AD output. |
26 |
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o verification/tutorial_tracer_adjsens: |
27 |
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- OpenAD test: switch to vector-invariant momentum since fluxform with |
28 |
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rStar causes problems with OpenAD; update output. |
29 |
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o tools: |
30 |
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- genmake2: define a common prefix for all temp-file names ; move them |
31 |
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to local /tmp disk (but would be easy to move them back); |
32 |
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- xmakedepend: apply the same switch for temp-files. |
33 |
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o pkg/offline: |
34 |
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- changes for use with rStar (NLFS): assume that we continue to provide |
35 |
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UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
36 |
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output files) and apply r* scaling at each time-step (function of the time |
37 |
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varying Eta field); use normal pickup files (needed for restart with NLFS). |
38 |
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o adjoint with OpenAD: |
39 |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
40 |
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package openad. This package has to be compiled for all runs with OpenAD |
41 |
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instead of specifying code_oad_all as a modification directory. |
42 |
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- link the fortran templates from tools/OAD_support to the build directory |
43 |
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for preprocessing to avoid conflicts between different setups compiled |
44 |
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simultaneously and simplify cleanup. |
45 |
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o pkg/exf: |
46 |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
47 |
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main model or other pkgs are exchanged in EXF_MAPFIELDS). |
48 |
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o model/src: |
49 |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
50 |
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(similar to do_fields_blocking_exchanges.F). |
51 |
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o tools/genmake2: |
52 |
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- remove TAF output src code just before calling staf (when not doing a fresh |
53 |
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built, will stop if things go wrong with staf). |
54 |
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- fix target "adobj" (left from TAF version-2 transition) |
55 |
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o pkg/diagnostics: |
56 |
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- add a parameter to track the status of pkg/diagnostics activation; |
57 |
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this replace/extend the use of logical param "settingDiags" (to check |
58 |
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when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
59 |
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New S/R to print error message and stop when pkgStatus is not right. |
60 |
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- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
61 |
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|
62 |
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checkpoint64m (2013/08/13) |
63 |
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o model/inc: |
64 |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
65 |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
66 |
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o pkg/kpp & aim_v23: |
67 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
68 |
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o pkg/seaice: |
69 |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
70 |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
71 |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
72 |
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o eesupp/src: |
73 |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
74 |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
75 |
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o switch to TAF version-2: |
76 |
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- add flow directives to "freeze" naming convention for ad-routines that |
77 |
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are used in I/O routines of adjoint state and associated common blocks |
78 |
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that are used in adcommon.h (backward compatible with version-1) |
79 |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
80 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
81 |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
82 |
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out except for diva). |
83 |
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- the major change with TAF version-2 is that both the differentiated |
84 |
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routines and the forward routines (new) are returned as part of the TAF |
85 |
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output source code. Update genmake2 accordingly. |
86 |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
87 |
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with version-2 when compared to TLM or FWD gradient); other experiments |
88 |
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output show minor changes (machine truncation level); update the few AD & |
89 |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
90 |
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|
91 |
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checkpoint64l (2013/08/05) |
92 |
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o model/src: |
93 |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
94 |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
95 |
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when using TAF but only if using OpenAD. |
96 |
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o pkg/mom_common+fluxform+vecinv: |
97 |
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- always set horiz. viscosity arrays to background value before calling |
98 |
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MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
99 |
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only when using variable horiz. viscosity (useVariableVisc=T); |
100 |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
101 |
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o pkg/mom_common: variable horiz. viscosity in NH code |
102 |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
103 |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
104 |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
105 |
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useBiharmonicVisc & useVariableVisc. |
106 |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
107 |
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in calc_gw.F, version 1.27, 2006/06/20): |
108 |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
109 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
110 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
111 |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
112 |
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any type of variable viscosity, e.g., viscAh/4Grid) |
113 |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
114 |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
115 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
116 |
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default viscAh,viscA4 is zero). |
117 |
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o model/src: |
118 |
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- extend length of drC & recip_drC from Nr to Nr+1. |
119 |
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o Divided Adjoint (DIVA) with MPI: |
120 |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
121 |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
122 |
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and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
123 |
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|
124 |
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checkpoint64k (2013/07/23) |
125 |
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o tools/OAD_support: |
126 |
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- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
127 |
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and remove it from genmake2. |
128 |
|
o tools/build_options: |
129 |
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- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
130 |
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MPI_HEADER_FILES list (let genmake2 find the missing headers) |
131 |
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o verification/halfpipe_streamice: |
132 |
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- change to driving stress formulation; update both Fwd & AD output. |
133 |
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o tools/genmake2 and Divided Adjoint with MPI: |
134 |
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- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
135 |
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- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
136 |
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- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
137 |
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Makefile, which is set by genmake2, and check which mpi-headers are needed. |
138 |
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Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
139 |
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- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
140 |
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o testreport: |
141 |
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- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
142 |
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perform additional runs (number of additional runs is "add_DIVA_runs" taken |
143 |
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from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
144 |
|
o verification/lab_sea (AD test): |
145 |
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- change to test Divided Adjoint Run in this set-up (both standard AD test |
146 |
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and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
147 |
|
o pkg atm_ & ocn_compon_interf: |
148 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
149 |
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staggerTimeStep implementation) and disable (retired) corresponding |
150 |
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parameter. |
151 |
|
o pkg/offline: |
152 |
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- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
153 |
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- add S/R OFFLINE_CHECK to print offline parameter summary |
154 |
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and stop if loading a file that is not used; |
155 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
156 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
157 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
158 |
|
for monitoring CFL numbers and checking offline fields. |
159 |
|
o OpenAD: |
160 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
161 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
162 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
163 |
|
o model/src: |
164 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
165 |
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(where external_forcing_adjust was called) and change list of arguments; |
166 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
167 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
168 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
169 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
170 |
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arrays in FFIELDS.h. |
171 |
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- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
172 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
173 |
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ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
174 |
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- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
175 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
176 |
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error in AD code). |
177 |
|
|
178 |
|
checkpoint64j (2013/07/04) |
179 |
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o pkg/offline: |
180 |
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- to enable the use of other features with pkg offline (e.g., obcs), |
181 |
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also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
182 |
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- comment out "allowFreezing" (now active) in 2 offline testing exp. |
183 |
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o pkg/exf ALLOW_RUNOFTEMP |
184 |
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- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
185 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
186 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
187 |
|
o pkg/atm_phys: |
188 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
189 |
|
o verification, ad-tests: |
190 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
191 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
192 |
|
o verification/halfpipe_streamice: |
193 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
194 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
195 |
|
verification results for forward test. |
196 |
|
- add adjoint test. |
197 |
|
o pkg/ptracers: |
198 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
199 |
|
o pkg/gmredi: |
200 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
201 |
|
- It uses mixing length theory and suppression by steering level effects to |
202 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
203 |
|
to JPO, for more details). |
204 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
205 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
206 |
|
- New files added to pkg/gmredi: |
207 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
208 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
209 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
210 |
|
for use in gmredi_k3d |
211 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
212 |
|
the eddy diffusivity |
213 |
|
|
214 |
|
checkpoint64i (2013/06/18) |
215 |
|
o pkg/cheapaml: |
216 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
217 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
218 |
|
with pkg/cheapaml. |
219 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
220 |
|
simple cs.pcol to plot 2D fields on a map |
221 |
|
o pkg/streamice: |
222 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
223 |
|
sheets and ice streams |
224 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
225 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
226 |
|
ed that this will change) |
227 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
228 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
229 |
|
rectangular embayment |
230 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
231 |
|
- for questions, email dgoldber@mit.edu |
232 |
|
o pkg/thsice: |
233 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
234 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
235 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
236 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
237 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
238 |
|
o pkg/cfc: |
239 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
240 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
241 |
|
- change some hard-coded constant to run time parameter for reading and |
242 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
243 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
244 |
|
- put arguments in standard order: myTime, myIter, myThid |
245 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
246 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
247 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
248 |
|
- new routine to print summary of CFC params and check for consistency. |
249 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
250 |
|
similar to thsice_advdiff. |
251 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
252 |
|
o pkg/cfc: |
253 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
254 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
255 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
256 |
|
hemisphere value. |
257 |
|
o pkg/seaice: |
258 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
259 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
260 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
261 |
|
- requires an additional time level that is stored in the pickup |
262 |
|
- you can start with AB2 from a pickup without this time level with |
263 |
|
pickupStrictlyMatch = .false. |
264 |
|
|
265 |
|
checkpoint64h (2013/05/26) |
266 |
|
o pkg/cheapaml: |
267 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
268 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
269 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
270 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
271 |
|
(Note: was already the case for Tair,Qair advection); |
272 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
273 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
274 |
|
- fill in array "Qsw" (for short-wave heating); |
275 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
276 |
|
before any update (consistent with MITgcm state var diagnostics); |
277 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
278 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
279 |
|
o pkg/seaice: |
280 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
281 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
282 |
|
- allows to compile pkg/seaice without pkg/exf. |
283 |
|
o tools/OAD_support: |
284 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
285 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
286 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
287 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
288 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
289 |
|
o pkg/offline: |
290 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
291 |
|
(previously called from pkg/dic_surfforcing_init.F) |
292 |
|
o model/src: |
293 |
|
- re-order sequence of calls within packages_init_variables.F, using |
294 |
|
standard order, except for: |
295 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
296 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
297 |
|
o new pkg: atm_phys |
298 |
|
- add entry point and source code (previously in contrib |
299 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
300 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
301 |
|
- re-order sequence of calls within packages_readparms.F, |
302 |
|
packages_init_fixed.F and packages_write_pickup.F |
303 |
|
(but skip packages_init_variables.F because of TAF issues). |
304 |
|
- update contrib/*/atm_gray/ experiment. |
305 |
|
o pkg/seaice (ITD code): |
306 |
|
- simplify and fix the writing of pickup-files for ITD case |
307 |
|
o pkg/seaice (ITD code): |
308 |
|
- introduce floe size dependent lateral melt for ITD case; |
309 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
310 |
|
- update seaice_itd experiment main output. |
311 |
|
o pkg/thsice: |
312 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
313 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
314 |
|
changed accordingly pkg/atm2d. |
315 |
|
|
316 |
|
checkpoint64g (2013/05/01) |
317 |
|
o pkg/exf ALLOW_RUNOFTEMP |
318 |
|
- if defined, river and glacier runoff temperature can be read-in from |
319 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
320 |
|
o pkg/thsice (& pkg/bulk_force): |
321 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
322 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
323 |
|
- change computation domain to always be the interior (without overlap). |
324 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
325 |
|
o verification/tutorial_global_oce_biogeo: |
326 |
|
- add preliminary OpenAD setup (still has problems) |
327 |
|
o pkg/seaice: |
328 |
|
- turn some parameters for choosing the convergence criterion of |
329 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
330 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
331 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
332 |
|
the results of lab_sea/input because a division has been replaced by |
333 |
|
a multiplication with the reciprocal (sumNorm) |
334 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
335 |
|
convergence of solver (changes results, of course), and to test some |
336 |
|
new features |
337 |
|
o model/src: |
338 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
339 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
340 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
341 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
342 |
|
o pkg/shelfice: |
343 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
344 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
345 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
346 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
347 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
348 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
349 |
|
- update isomip experiment forward output (get machine truncation error |
350 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
351 |
|
o verification/offline_exf_seaice: |
352 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
353 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
354 |
|
SEAICE_growMeltByConv = .TRUE., |
355 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
356 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
357 |
|
o verification/global_ocean.cs32x15: |
358 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
359 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
360 |
|
o verification/offline_exf_seaice: |
361 |
|
- adjust list of tested variables (with testreport) and update |
362 |
|
standard test output with better slection of monitored fields. |
363 |
|
o pkg/cd_code: |
364 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
365 |
|
experiment lab_sea.hb87 |
366 |
|
o tools/genmake2: |
367 |
|
- change default makedepend from the system default to tools/xmakedepend: |
368 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
369 |
|
otherwise select the system default (if exist and pass the test) or |
370 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
371 |
|
o pkg/exf & pkg/thsice: |
372 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
373 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
374 |
|
1) Rain has same temp as Air. |
375 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
376 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
377 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
378 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
379 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
380 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
381 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
382 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
383 |
|
o pkg/thsice: |
384 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
385 |
|
implementation): move THSICE_AVE call after the advection (called directly |
386 |
|
from thsice_do_advect.F). |
387 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
388 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
389 |
|
multiDimAdvection=.FALSE., |
390 |
|
There is still an issue with this. |
391 |
|
o pkg/thsice: |
392 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
393 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
394 |
|
and offline_exf_seaice (main test). |
395 |
|
|
396 |
|
checkpoint64f (2013/03/31) |
397 |
|
o verification/OpenAD: |
398 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
399 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
400 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
401 |
|
o verification/tutorial_global_oce_biogeo: |
402 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
403 |
|
o verification/offline_exf_seaice: |
404 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
405 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
406 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
407 |
|
o pkg/seaice/seaice_evp.F: |
408 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
409 |
|
the turningAngle is non-zero) over open water to avoid stripes |
410 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
411 |
|
the verification experiment (because turningAngle=0 in that experiment), |
412 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
413 |
|
o verification, AD & TLM output: |
414 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
415 |
|
additions and multiplications which affect results at machine truncation |
416 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
417 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
418 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
419 |
|
digits of matching. |
420 |
|
o pkg/seaice: |
421 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
422 |
|
"zebra" method: split vector loop into two with step size 2; this |
423 |
|
solves a general convergence problem for the JFNK solver on a vector |
424 |
|
computer. It has the potential to even improve convergence for |
425 |
|
non-vector machines, but it does change the results so it is turned |
426 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
427 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
428 |
|
|
429 |
|
checkpoint64e (2013/03/05) |
430 |
|
o pkg/ecco and several verification experiments: |
431 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
432 |
|
from ecco package, and revert to unified routine in model/src/ |
433 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
434 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
435 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
436 |
|
o pkg/generic_advdiff: |
437 |
|
- implement compressible flow method for multi-dim advection (similar to |
438 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
439 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
440 |
|
vertical advection. |
441 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
442 |
|
to test compressible flow multi-dim advection. |
443 |
|
o pkg/generic_advdiff: |
444 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
445 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
446 |
|
o pkg/seaice: |
447 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
448 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
449 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
450 |
|
seaice_calc_strainrates.F; |
451 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
452 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
453 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
454 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
455 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
456 |
|
- new subroutines seaice_lsr_tridiagu/v |
457 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
458 |
|
additive Schwarz method, but not used for now. |
459 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
460 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
461 |
|
o OpenAD support |
462 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
463 |
|
OpenAD revolve loop replacement |
464 |
|
(new S/R main_do_loop.F) |
465 |
|
o model/src: |
466 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
467 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
468 |
|
ADAMS_BASHFORTH2. |
469 |
|
o pkg/cheapaml: |
470 |
|
- add new parameter (default=F, same as before) to disable full domain |
471 |
|
(including land) periodicity in X & Y dir. |
472 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
473 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
474 |
|
into single S/R CHEAPAML_TIMESTEP. |
475 |
|
|
476 |
|
checkpoint64d (2013/02/17) |
477 |
|
o pkg/monitor (angular momentum): |
478 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
479 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
480 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
481 |
|
each component (instead of from cell centered averaged) and use the 4 |
482 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
483 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
484 |
|
FreeSurf) if using vectorInvariant momentum. |
485 |
|
o model/src (horizontal grid): |
486 |
|
- move initialisation of all horizontal grid arrays to null value |
487 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
488 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
489 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
490 |
|
compute them in S/R CALC_GRID_ANGLES. |
491 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
492 |
|
SEAICE_JFNK_tolIter |
493 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
494 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
495 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
496 |
|
- extend loop range in seaice_calc_viscosity |
497 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
498 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
499 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
500 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
501 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
502 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
503 |
|
for output.dyn_jfnk.txt |
504 |
|
in seaice_fgmres.F (unrelated to RAS) |
505 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
506 |
|
efficient), but because this changes the results, turn it off by |
507 |
|
default |
508 |
|
- replace the save statement by local common blocks |
509 |
|
o utils/matlab: |
510 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
511 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
512 |
|
instead of local script "load_cs.m". |
513 |
|
o pkg/seaice: |
514 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
515 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
516 |
|
change the verification experiment, because of the particular domain |
517 |
|
decomposition |
518 |
|
o pkg/diagnostics: |
519 |
|
- change default missing_value from UNSET_RL to -999. |
520 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
521 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
522 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
523 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
524 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
525 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
526 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
527 |
|
- moved the search algorithm into a separate subroutine, that is kept |
528 |
|
within the same file for automatic inlining. |
529 |
|
- modified catching potential errors |
530 |
|
o pkg/ecco: |
531 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
532 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
533 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
534 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
535 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
536 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
537 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
538 |
|
o model/src: |
539 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
540 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
541 |
|
and cpl_aim+ocn. |
542 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
543 |
|
for fizhi-cs experiments reference output. |
544 |
|
o pkg/ctrl: |
545 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
546 |
|
ALLOW_GENTIM2D_CONTROL |
547 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
548 |
|
o verification/global_ocean.cs32x15: |
549 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
550 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
551 |
|
o pkg/ptracers: |
552 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
553 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
554 |
|
o pkg/thsice: |
555 |
|
- implement new sequence of calls for thsice+seaice: |
556 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
557 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
558 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
559 |
|
in CPP_OPTIONS.h) to recover old sequence; |
560 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
561 |
|
just before advection (instead of just after advection in old sequence); |
562 |
|
- update output of experiment offline_exf_seaice (standard test); |
563 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
564 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
565 |
|
o pkg/aim_v23: |
566 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
567 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
568 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
569 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
570 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
571 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
572 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
573 |
o pkg/thsice: |
o pkg/thsice: |
574 |
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
575 |
where just seaice diffusion is used without seaice-dynamics. |
where just seaice diffusion is used without seaice-dynamics. |