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revision 1.2072 by dimitri, Thu Sep 25 00:40:49 2014 UTC revision 1.2117 by jmc, Fri Jan 23 01:45:07 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 model/src:
8      - change units of frictionHeating field from W to W/m^2
9      - fix bug in frictional heating from stratospheric drag in
10        S/R ATM_PHYS_TENDENCY_APPLY_V
11      - with synchronous time-stepping: move resetting to zero of frictionHeating
12        field from load_fields_driver.F to thermodynamics.F ;
13      - add diagnostics for frictional heating.
14    o model/src & gmredi K3D:
15      - add frictionHeating field to pickup-files (for synchronous time-stepping)
16      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
17      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
18        and name in pickup file).
19      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
20    o model/src:
21      - move (from ini_forcing.F) initialisation of all arrays in header file
22        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
23        (since Nov 2012) with option selectAddFluid=1.
24    o pkg/shelfice:
25      - change units (+ document) of newly added field "shelfIceMassDynTendency"
26      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
27    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
28    o pkg/seaice: two new runtime parameters:
29      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
30        long overdue
31      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
32        parameterization of tensil stress for fast ice (does not do anything yet)
33    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
34        for LSR: move checking overlaps out of JFNK-if-block
35    o pkg/atm_phys:
36      - move copy of grid and dynamical fields out of atm_phys_driver.F into
37        new S/R ATM_PHYS_DYN2PHYS.
38      - fix level height for Linear Free-Surf case (to be consistent with
39        fixed-in-time pressure levels).
40    o pkg/mom_common (bottomdrag):
41      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
42        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
43        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
44    o pkg/shelfice (u/v_drag):
45      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
46      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
47        (now similar to shelfice_u_drag.F)
48      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
49        from mom_vecinv.F (similar to mom_fluxform calls).
50    o pkg/mom_common (bottomdrag):
51      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
52      - add options for alternative discretisation of velocity norm in quadratic
53        bottom drag: averaging of grid-cell-center KE to U.point and V.point
54        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
55        improves when averaging only the other component (e.g. vVel for U bottom
56        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
57      - add options (bottomVisc_pCell) to account for partial-cell in bottom
58        friction (no-slip BC) thus getting the true distance from the bottom;
59        off by default since this also reduces model stability (explicit bottom
60        friction). Changes produce different machine truncation with linear-drag
61        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
62        front_relax (bvp & mxl, 10 & 11 digits).
63    o model/src & mom pkgs:
64      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
65        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
66      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
67        just copy level Nr value to level Nr+1.
68    o doc:
69      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
70    o pkg/streamice:
71      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
72        SHELFICE.h: move array shelficemass to init_varia, initialise
73        from array shelficemassinit, which is set in init_fixed and
74        has option to be set from file; introduce array
75        shelficeMassDynTend array, set thru file in init_fixed
76      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
77        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
78        pkg/streamice
79      - shelfice_thermodynamics.F: call shelfice_step_icemass if
80        SHELFICEMassStepping = .true.
81      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
82    
83    checkpoint65h (2014/12/17)
84    o verification/global_ocean.90x40x15, global_ocean_ebm:
85      - update to generic controls.
86    o pkg/ctrl:
87      - ctrl_map_ini_genarr.F: test for igen>0
88      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
89      - move gentim2d part of ctrl_map_ini_genarr.F to
90        new separate routine : ctrl_map_ini_gentim2d.F
91      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
92        add time variable weights and cyclic controls (time mean,
93        seasonal cycle, etc) capabilities to gentim2d
94    o pkg/ecco:
95      - move reading of error, conversion to weights from
96        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
97    o global_oce_llc90, cs32:
98      - activte sbo.
99      - CTRL_SIZE.h : add maxCtrlProc.
100      - activate the new genctrl capabilities.
101      - update following reorganization of global_oce_input_fields.tar.gz  
102    o pkg/ctrl/ctrl_ad_diff.list:
103      - add missing ctrl_init_rec.f
104    o tools/OAD_support/keepOriginal:
105      - add ctrl_init_rec.F
106    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
107      - avoid recomputations of xx_gentim2d_dummy.
108    o momentum diagnostics:
109      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
110        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
111    o pkg/seaice/seaice_lsr.F:
112      - fix computation of BU/BV, make sure they are non-zero, only necessary
113        for cubed sphere exchanges and SEAICE_OLx/y>0.
114        This makes calling s/r fill_cs_corner_rl obsolete (removed).
115    o verification/global_ocean.cs32x15/input.seaice
116      - add test for strong implicit coupling and restricted addtive Schwarz
117        methods for LSR
118      - update results/output.seaice.txt
119    o verification/tutorial_global_oce_biogeo:
120      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
121        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
122        update output_adm,_oadm,_tlm.txt
123    o pkg/dic:
124      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
125      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
126        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
127    o verification/tutorial_global_oce_biogeo:
128      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
129        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
130        update output_adm,_oadm,_tlm.txt
131    o eesupp/src:
132      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
133        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
134    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
135      LSR (following Hutchings et al. 2004)
136      - introduce zetaZ as a global variable (requires adjustments in
137        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
138        in seaice_calc_viscosities.F
139      - new flag SEAICEuseStrImpCpl (default off)
140      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
141        momentum equations
142      - JFNK-solver (preconditioner) adjusted to allow using this method
143        (where it does not have any positive effect)
144    o pkg/seaice
145      - add overlap for restrictive additive Schwartz method also to LSR, but
146        turn it off by default (because it only seems to work for non-cubed
147        sphere/llc topologies)
148    o pkg/autodiff
149      - add extra exchanges in addummy_in_steppging also for mnc output
150    o pkg/seaice:
151      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
152        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
153  o pkg/obcs:  o pkg/obcs:
154    - add additional compile-time options for sponge boundary layers    - add option to specify domain-connected piece Id along OB though files
155        (for now, only used to diagnose PhiVel; default =1 -> global correction)
156      - modify obcs_diag_balance.F to process each connected-part separately;
157        exclude OB where Id = 0 but keep the full divergence there (-> constant
158        Psi along this portion of OB and all inflow derived from grad(Phi))
159      - add example of OB-conect files in verification/so_box_biogeo/input.
160    o pkg/diagnostics:
161      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
162      a) use non zero matrix element across OB and solve for Phi 1 grid point
163         outside OB (i.e, where tracer OBCS are applied).
164      b) global imbalance of inFlow/outFlow across OB: instead of modifying
165         velocity across OB, spread it uniformly along the OB in the RHS.
166    
167    checkpoint65g (2014/11/19)
168    o pkg/diagnostcis:
169      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
170    o pkg/my82,pp81,kl10:
171      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
172        field diffKr as background diffusivity to set minimum diffusivity value.
173    o pkg/seaice:
174      - add new parameter SEAICEuseEVPrev (for revisited EVP by
175        Bouillon et al 2013)
176      - add SEAICE_evpAlpha/Beta to namelist
177      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
178        involve trivial re-ordering of divisions/multiplications that should not
179        have any effects, but ... they do change the results of lab_sea.hb87 so
180        that only 2 digits of agreement remain, in line with the general
181        instability/fragility of the evp-code. For now, I do not care and just
182        update the verification experiment
183    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
184      - remove xx_genarr2d_numsmooth etc
185      - use xx_genarr2d_preproc etc instead
186      - carry out smooth_correl2D at initialization stage rather than during
187        time stepping.
188      - get smoothOpNb from xx_gentim2d_preproc
189    o global_oce_cs32 :
190      - add test of generic ecco capabilities.
191    o pkg/exf/exf_getsurfacefluxes.F :
192      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
193    o pkg/ctrl,ecco :
194      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
195        is defined.
196    o pkg/seaice: add diagnostics for Delta (deformation parameter)
197    o model/src:
198      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
199        diffusivity (background) is specified but ignored.
200    o verification:
201      - in testreport, convert hostname to lower case for default output dir name
202    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
203    o pkg/dic: add modifications from Hajoon:
204      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
205      - light attenuation: add self-shading effect by climatological Chlorophyll
206        (read from file).
207    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
208        compiles when SEAICE_ALLOW_DYNAMICS is undefined
209    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
210        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
211        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
212        approach where CPP_OPTIONS.h includes an omnipotent
213        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
214    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
215        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
216    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
217        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
218        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
219    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
220      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
221      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
222      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
223      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
224    o pkg/ctrl,ecco,exf :
225      - remove variables associated with NON-generic costs,
226        unless ECCO_CTRL_DEPRECATED is defined.
227      - remove NON-generic NON-obcs controls,
228        unless ECCO_CTRL_DEPRECATED is defined.
229    o pkg/ctrl : added ctrl_local_params.h
230    o pkg/ecco : added ecco_local_params.h
231    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
232        experiments, which will progressively be removed once the
233        experiments are revised to use only generic controls/costs.
234    
235    checkpoint65f (2014/10/13)
236    o pkg/ctrl, ecco, seaice : minor changes in headers
237    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
238        cost function and control capabilities added since checkpoint65c.
239    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
240    o pkg/ecco: increase modularity and improve logic
241      - ecco_toolbox.F (new) : basic operations that are often used,
242        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
243        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
244      - cost_gencal.F (new) : determine filnames and records.
245      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
246      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
247        and exploit the above functions leading to more compact code.
248      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
249      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
250        using_ers, using_gfo, using_mdt is now only defined within gencost)
251    o pkg/ecco: extend generic cost capabilities
252      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
253        capabilities via gencost_preproc (+ _c,_i,_r related params),
254        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
255        gencost_outputlevel arguments to cost_generic
256      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
257        and active_read, making room for gencost_preproc to take effect.
258        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
259      - pkg/ecco/cost_generic.F :
260        compute and store misfit maks*(model-data) in localdif that is
261        then used in cost and for output, output misfit if outlev.GT.0
262      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
263        rather gencost_barfile for deciding whether to write barfile
264      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
265      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
266        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
267      - pkg/ecco/ecco_summary.F : report gencost variables
268      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
269    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
270    o pkg/ecco: internal re-organization
271      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
272        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
273        mv relevant variables definition from ecco_cost.h to ecco.h,
274        make sure gencost routines only include ecco.h)
275      - throughout : add missing CCP switches, rm unused variables,
276        and rm un-necessary CPP switches
277      - throughout gencost routines : replace modelstartdate with
278        gencost_startdate when needed
279      - cost_bp_read.F : use arguments, instead of common blocs
280        so that it can be used also by (new) cost_gencost_bpv4.F
281      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
282      - ecco_phys.F : compute etanFull
283      - ecco_readparms.F : rename using_topex as using_tpj, add
284        bpv4-grace to gencost list, initialize added parameters
285      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
286    
287    checkpoint65e (2014/09/28)
288    o pkg/obcs:
289      - replaced the just-added CPP options with run-time variables
290        (see pkg/obcs/OBCS_PARAMS.h for details)
291    o pkg/obcs:
292      - add additional CPP options for sponge boundary layers
293      (see pkg/obcs/OBCS_OPTIONS.h for details)      (see pkg/obcs/OBCS_OPTIONS.h for details)
294  o pkg/atm_phys:  o pkg/atm_phys:
295    - implement simple (obliquity only, assuming circular planet orbit)    - implement simple (obliquity only, assuming circular planet orbit)
296      seasonal cycle for incoming insolation ; used when run-time parameter      seasonal cycle for incoming insolation ; used when run-time parameter
297      "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.      "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
298  o pkg/exf, pkg/ecco, pkg/ctrl:  o pkg/exf, pkg/ecco, pkg/ctrl:
299      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets    - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
300      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip    - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
301      - implement gentim2d for xx_tauu, xx_tauv    - implement gentim2d for xx_tauu, xx_tauv
302  o pkg/ctrl, pkg/ecco :  o pkg/ctrl, pkg/ecco :
303      - fix and complement the generic controls implementation    - fix and complement the generic controls implementation
304  o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,  o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
305      pkg/shelfice/shelfice_thermodynamics.F,      pkg/shelfice/shelfice_thermodynamics.F,
306      verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,      verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
# Line 311  o pkg/seaice: more clean up Line 595  o pkg/seaice: more clean up
595      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
596      this experiment):      this experiment):
597      > size mitgcmuv_ad      > size mitgcmuv_ad
598      text    data        bss     dec        hex        text    data        bss     dec        hex
599      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
600      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
601      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
602      text    data        bss     dec        hex      text    data        bss     dec        hex

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