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revision 1.2103 by mlosch, Tue Dec 9 14:17:23 2014 UTC revision 1.2139 by mlosch, Tue Mar 3 15:57:00 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o verification/testreport:
8      - replace "grep -A3" with POSIX conformal sed command, because there are
9        implementations of grep that cannot do contextual searches
10      - replace "cat -n" by "nl" (two occurrences), because not all implementations
11        of "cat" have the option "-n"
12    o model/src: add new file gsw_teos10.F that contains
13        3 functions, more or less a copy of the gsw_toolbox.f90 of the TEOS-10
14        fortran interface, that are used to convert from conservative to
15        potential temperature. For now they are not called anywhere.
16    o pkg/ggl90: make "useIDEMIX" useful
17      - re-organize code in s/r ggl90_calc a little to move computations that
18        are different for idemix into separate loops (changes verification
19        experiment idemix at truncation level, 12 digits remain -> updated)
20      - requires 2 new 2D fields KappaM, verticalShear
21      - make hFacI and recip_hFacI local 3D variables that are passed to
22        s/r ggl90_idemix
23      - fix and improve some comments
24    
25    checkpoint65j (2015/02/25)
26    o pkg/openad
27      - synchronize seawater.F with version in model/src: replace routine
28        body of sw_temp by calling sw_ptmp and fix/add a few comments.
29    o pkg/mnc:
30      - change default value of pickup_read/write_mnc params to FALSE
31        (since few features are missing in reading MNC pickup files).
32    o model/src:
33      - change default (background) vertical diffusivity for salt to be the
34        temperature (background) vertical diffusivity.
35      - change background vertical diffusivity in vertical mixing pkgs ggl90,
36        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
37        This makes ptracers default diffusivity (that uses salt diffKr) more
38        consistent with vertical mixing schemes.
39    o verification/testreport:
40      - fix typo in "-pcls" option ;
41      - put temp files in /tmp (instead of in local dir)
42      - add option "-ncad" to use genmake2 new option "-nocat4ad"
43      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
44    o pkg/ggl90 (idemix code):
45      - apply few fixes ; add some missing "_d 0" ; update output of exp.
46        global_ocean.90x40x15.idemix
47    o OpenAD
48      - enable active file I/O and begin removal of work-around code
49        for OpenAD for handling control variables (memory vs. active files)
50      - new CPP options file OPENAD_OPTIONS.h
51      - revert to genarr2d gradient check for hs94.1x64x5
52      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
53      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
54    o tools/genmake2:
55      - add option for an alternative Makefile (from Martin) where multiple
56        source files are sent to TAF (instead of all in one file).
57    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
58      - code provided by Carsten Eden as an extension of ggl90
59      - so far the code is turned on within ggl90 by setting a CPP-flag at
60        compile time; a runtime flag implementation is not yet complete
61      - tested in new verification experiment global_ocean.90x40x15.idemix
62    o verification:
63      - reduce length of the AD test run by half for experiments
64        global_ocean.cs32x15 (std + thsice) and isomip
65      - enable active file I/O for OpenAD, adjust verifications accordingly
66      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
67    o verification/testreport:
68      - fix two non-POSIX sed statements so that there are no error messages
69        on Mac OS X
70      - replace hostname -s with hostname | sed 's/\..*$//'
71    o model/src/seawater.F:
72      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
73        (following the matlab code), which would have avoided the bug caught
74        by Matt (see below) in the first place
75    o pkg/shelfice:
76      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
77        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
78      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
79        ice-shelf case (i.e., within surface level).
80      - add config summary in shelfice_check.F
81      - remove global variable recip_SHELFICElatentHeat and replace by a local
82        variable recip_latentHeat
83      - introduce diagnostics for friction velocity uStar (in case of
84        SHELFICEuseGammaFrict)
85      - change verification experiment isomip.htd:
86        + start from pickup (as input_ad at nIter0=8640)
87        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
88        + test SHELFICEuseGammaFrict = .TRUE.
89        + test SHELFICEadvDiffHeatFlux = .TRUE.
90    o model/src:
91      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
92        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
93        update output of experiments global_with_exf.yearly and isomip (all 6).
94    o pkg/shelfice:
95      - change setting of kTopC to also be zero where there is no ice-shelf.
96      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
97        ice-shelf is.
98      - first attempt to get RealFreshWaterFlux effects: for now, only without
99        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
100    o pkg/seaice: add the option to prescribe a fixed thickness PDF
101      for thermodynamic calculations
102      - because of divisions of the type 7/7 not exactly equal to 1, this change
103        affects results of some verification experiments by up to 4 digits:
104        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
105        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
106        adjoint: lab_sea, lab_sea.noseaicedyn
107        -> updated
108    
109    checkpoint65i (2015/01/23)
110    o model/src:
111      - change units of frictionHeating field from W to W/m^2
112      - fix bug in frictional heating from stratospheric drag in
113        S/R ATM_PHYS_TENDENCY_APPLY_V
114      - with synchronous time-stepping: move resetting to zero of frictionHeating
115        field from load_fields_driver.F to thermodynamics.F ;
116      - add diagnostics for frictional heating.
117    o model/src & gmredi K3D:
118      - add frictionHeating field to pickup-files (for synchronous time-stepping)
119      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
120      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
121        and name in pickup file).
122      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
123    o model/src:
124      - move (from ini_forcing.F) initialisation of all arrays in header file
125        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
126        (since Nov 2012) with option selectAddFluid=1.
127    o pkg/shelfice:
128      - change units (+ document) of newly added field "shelfIceMassDynTendency"
129      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
130    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
131    o pkg/seaice: two new runtime parameters:
132      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
133        long overdue
134      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
135        parameterization of tensil stress for fast ice (does not do anything yet)
136    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
137        for LSR: move checking overlaps out of JFNK-if-block
138    o pkg/atm_phys:
139      - move copy of grid and dynamical fields out of atm_phys_driver.F into
140        new S/R ATM_PHYS_DYN2PHYS.
141      - fix level height for Linear Free-Surf case (to be consistent with
142        fixed-in-time pressure levels).
143    o pkg/mom_common (bottomdrag):
144      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
145        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
146        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
147    o pkg/shelfice (u/v_drag):
148      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
149      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
150        (now similar to shelfice_u_drag.F)
151      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
152        from mom_vecinv.F (similar to mom_fluxform calls).
153    o pkg/mom_common (bottomdrag):
154      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
155      - add options for alternative discretisation of velocity norm in quadratic
156        bottom drag: averaging of grid-cell-center KE to U.point and V.point
157        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
158        improves when averaging only the other component (e.g. vVel for U bottom
159        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
160      - add options (bottomVisc_pCell) to account for partial-cell in bottom
161        friction (no-slip BC) thus getting the true distance from the bottom;
162        off by default since this also reduces model stability (explicit bottom
163        friction). Changes produce different machine truncation with linear-drag
164        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
165        front_relax (bvp & mxl, 10 & 11 digits).
166    o model/src & mom pkgs:
167      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
168        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
169      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
170        just copy level Nr value to level Nr+1.
171    o doc:
172      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
173    o pkg/streamice:
174      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
175        SHELFICE.h: move array shelficemass to init_varia, initialise
176        from array shelficemassinit, which is set in init_fixed and
177        has option to be set from file; introduce array
178        shelficeMassDynTend array, set thru file in init_fixed
179      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
180        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
181        pkg/streamice
182      - shelfice_thermodynamics.F: call shelfice_step_icemass if
183        SHELFICEMassStepping = .true.
184      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
185    
186    checkpoint65h (2014/12/17)
187    o verification/global_ocean.90x40x15, global_ocean_ebm:
188      - update to generic controls.
189    o pkg/ctrl:
190      - ctrl_map_ini_genarr.F: test for igen>0
191      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
192      - move gentim2d part of ctrl_map_ini_genarr.F to
193        new separate routine : ctrl_map_ini_gentim2d.F
194      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
195        add time variable weights and cyclic controls (time mean,
196        seasonal cycle, etc) capabilities to gentim2d
197    o pkg/ecco:
198      - move reading of error, conversion to weights from
199        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
200    o global_oce_llc90, cs32:
201      - activte sbo.
202      - CTRL_SIZE.h : add maxCtrlProc.
203      - activate the new genctrl capabilities.
204      - update following reorganization of global_oce_input_fields.tar.gz  
205    o pkg/ctrl/ctrl_ad_diff.list:
206      - add missing ctrl_init_rec.f
207    o tools/OAD_support/keepOriginal:
208      - add ctrl_init_rec.F
209    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
210      - avoid recomputations of xx_gentim2d_dummy.
211    o momentum diagnostics:
212      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
213        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
214    o pkg/seaice/seaice_lsr.F:
215      - fix computation of BU/BV, make sure they are non-zero, only necessary
216        for cubed sphere exchanges and SEAICE_OLx/y>0.
217        This makes calling s/r fill_cs_corner_rl obsolete (removed).
218  o verification/global_ocean.cs32x15/input.seaice  o verification/global_ocean.cs32x15/input.seaice
219    - add test for strong implicit coupling and restricted addtive Schwarz    - add test for strong implicit coupling and restricted addtive Schwarz
220      methods for LSR      methods for LSR

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