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revision 1.2085 by gforget, Tue Oct 21 14:22:26 2014 UTC revision 1.2127 by mlosch, Thu Feb 19 16:37:58 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 global_oce_llc90,cs32 : ecco_v4 verification exps now use separate  o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013, Eden and Olbers, 2014)
8    AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than    - code provided by Carsten Eden as an extension of ggl90
9    ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,    - so far the code is turned on within ggl90 by setting a CPP-flag at
10    approach where CPP_OPTIONS.h includes an omnipotent      compile time; a runtime flag implementation is not yet complete
11    ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').    - tested in new verification experiment global_ocean.90x40x15.idemix
12  o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where  o verification:
13    ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.    - reduce length of the AD test run by half for experiments
14        global_ocean.cs32x15 (std + thsice) and isomip
15    o verification/testreport:
16      - fix two non-POSIX sed statements so that there are no error messages
17        on Mac OS X
18      - replace hostname -s with hostname | sed 's/\..*$//'
19    o model/src/seawater.F:
20      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
21        (following the matlab code), which would have avoided the bug caught
22        by Matt (see below) in the first place
23    o pkg/shelfice:
24      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
25        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
26      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
27        ice-shelf case (i.e., within surface level).
28      - add config summary in shelfice_check.F
29      - remove global variable recip_SHELFICElatentHeat and replace by a local
30        variable recip_latentHeat
31      - introduce diagnostics for friction velocity uStar (in case of
32        SHELFICEuseGammaFrict)
33      - change verification experiment isomip.htd:
34        + start from pickup (as input_ad at nIter0=8640)
35        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
36        + test SHELFICEuseGammaFrict = .TRUE.
37        + test SHELFICEadvDiffHeatFlux = .TRUE.
38    o model/src:
39      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
40        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
41        update output of experiments global_with_exf.yearly and isomip (all 6).
42    o pkg/shelfice:
43      - change setting of kTopC to also be zero where there is no ice-shelf.
44      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
45        ice-shelf is.
46      - first attempt to get RealFreshWaterFlux effects: for now, only without
47        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
48    o pkg/seaice: add the option to prescribe a fixed thickness PDF
49      for thermodynamic calculations
50      - because of divisions of the type 7/7 not exactly equal to 1, this change
51        affects results of some verification experiments by up to 4 digits:
52        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
53        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
54        adjoint: lab_sea, lab_sea.noseaicedyn
55        -> updated
56    
57    checkpoint65i (2015/01/23)
58    o model/src:
59      - change units of frictionHeating field from W to W/m^2
60      - fix bug in frictional heating from stratospheric drag in
61        S/R ATM_PHYS_TENDENCY_APPLY_V
62      - with synchronous time-stepping: move resetting to zero of frictionHeating
63        field from load_fields_driver.F to thermodynamics.F ;
64      - add diagnostics for frictional heating.
65    o model/src & gmredi K3D:
66      - add frictionHeating field to pickup-files (for synchronous time-stepping)
67      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
68      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
69        and name in pickup file).
70      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
71    o model/src:
72      - move (from ini_forcing.F) initialisation of all arrays in header file
73        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
74        (since Nov 2012) with option selectAddFluid=1.
75    o pkg/shelfice:
76      - change units (+ document) of newly added field "shelfIceMassDynTendency"
77      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
78    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
79    o pkg/seaice: two new runtime parameters:
80      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
81        long overdue
82      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
83        parameterization of tensil stress for fast ice (does not do anything yet)
84    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
85        for LSR: move checking overlaps out of JFNK-if-block
86    o pkg/atm_phys:
87      - move copy of grid and dynamical fields out of atm_phys_driver.F into
88        new S/R ATM_PHYS_DYN2PHYS.
89      - fix level height for Linear Free-Surf case (to be consistent with
90        fixed-in-time pressure levels).
91    o pkg/mom_common (bottomdrag):
92      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
93        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
94        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
95    o pkg/shelfice (u/v_drag):
96      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
97      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
98        (now similar to shelfice_u_drag.F)
99      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
100        from mom_vecinv.F (similar to mom_fluxform calls).
101    o pkg/mom_common (bottomdrag):
102      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
103      - add options for alternative discretisation of velocity norm in quadratic
104        bottom drag: averaging of grid-cell-center KE to U.point and V.point
105        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
106        improves when averaging only the other component (e.g. vVel for U bottom
107        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
108      - add options (bottomVisc_pCell) to account for partial-cell in bottom
109        friction (no-slip BC) thus getting the true distance from the bottom;
110        off by default since this also reduces model stability (explicit bottom
111        friction). Changes produce different machine truncation with linear-drag
112        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
113        front_relax (bvp & mxl, 10 & 11 digits).
114    o model/src & mom pkgs:
115      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
116        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
117      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
118        just copy level Nr value to level Nr+1.
119    o doc:
120      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
121    o pkg/streamice:
122      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
123        SHELFICE.h: move array shelficemass to init_varia, initialise
124        from array shelficemassinit, which is set in init_fixed and
125        has option to be set from file; introduce array
126        shelficeMassDynTend array, set thru file in init_fixed
127      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
128        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
129        pkg/streamice
130      - shelfice_thermodynamics.F: call shelfice_step_icemass if
131        SHELFICEMassStepping = .true.
132      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
133    
134    checkpoint65h (2014/12/17)
135    o verification/global_ocean.90x40x15, global_ocean_ebm:
136      - update to generic controls.
137    o pkg/ctrl:
138      - ctrl_map_ini_genarr.F: test for igen>0
139      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
140      - move gentim2d part of ctrl_map_ini_genarr.F to
141        new separate routine : ctrl_map_ini_gentim2d.F
142      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
143        add time variable weights and cyclic controls (time mean,
144        seasonal cycle, etc) capabilities to gentim2d
145    o pkg/ecco:
146      - move reading of error, conversion to weights from
147        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
148    o global_oce_llc90, cs32:
149      - activte sbo.
150      - CTRL_SIZE.h : add maxCtrlProc.
151      - activate the new genctrl capabilities.
152      - update following reorganization of global_oce_input_fields.tar.gz  
153    o pkg/ctrl/ctrl_ad_diff.list:
154      - add missing ctrl_init_rec.f
155    o tools/OAD_support/keepOriginal:
156      - add ctrl_init_rec.F
157    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
158      - avoid recomputations of xx_gentim2d_dummy.
159    o momentum diagnostics:
160      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
161        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
162    o pkg/seaice/seaice_lsr.F:
163      - fix computation of BU/BV, make sure they are non-zero, only necessary
164        for cubed sphere exchanges and SEAICE_OLx/y>0.
165        This makes calling s/r fill_cs_corner_rl obsolete (removed).
166    o verification/global_ocean.cs32x15/input.seaice
167      - add test for strong implicit coupling and restricted addtive Schwarz
168        methods for LSR
169      - update results/output.seaice.txt
170    o verification/tutorial_global_oce_biogeo:
171      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
172        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
173        update output_adm,_oadm,_tlm.txt
174    o pkg/dic:
175      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
176      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
177        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
178    o verification/tutorial_global_oce_biogeo:
179      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
180        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
181        update output_adm,_oadm,_tlm.txt
182    o eesupp/src:
183      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
184        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
185    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
186      LSR (following Hutchings et al. 2004)
187      - introduce zetaZ as a global variable (requires adjustments in
188        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
189        in seaice_calc_viscosities.F
190      - new flag SEAICEuseStrImpCpl (default off)
191      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
192        momentum equations
193      - JFNK-solver (preconditioner) adjusted to allow using this method
194        (where it does not have any positive effect)
195    o pkg/seaice
196      - add overlap for restrictive additive Schwartz method also to LSR, but
197        turn it off by default (because it only seems to work for non-cubed
198        sphere/llc topologies)
199    o pkg/autodiff
200      - add extra exchanges in addummy_in_steppging also for mnc output
201    o pkg/seaice:
202      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
203        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
204    o pkg/obcs:
205      - add option to specify domain-connected piece Id along OB though files
206        (for now, only used to diagnose PhiVel; default =1 -> global correction)
207      - modify obcs_diag_balance.F to process each connected-part separately;
208        exclude OB where Id = 0 but keep the full divergence there (-> constant
209        Psi along this portion of OB and all inflow derived from grad(Phi))
210      - add example of OB-conect files in verification/so_box_biogeo/input.
211    o pkg/diagnostics:
212      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
213      a) use non zero matrix element across OB and solve for Phi 1 grid point
214         outside OB (i.e, where tracer OBCS are applied).
215      b) global imbalance of inFlow/outFlow across OB: instead of modifying
216         velocity across OB, spread it uniformly along the OB in the RHS.
217    
218    checkpoint65g (2014/11/19)
219    o pkg/diagnostcis:
220      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
221    o pkg/my82,pp81,kl10:
222      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
223        field diffKr as background diffusivity to set minimum diffusivity value.
224    o pkg/seaice:
225      - add new parameter SEAICEuseEVPrev (for revisited EVP by
226        Bouillon et al 2013)
227      - add SEAICE_evpAlpha/Beta to namelist
228      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
229        involve trivial re-ordering of divisions/multiplications that should not
230        have any effects, but ... they do change the results of lab_sea.hb87 so
231        that only 2 digits of agreement remain, in line with the general
232        instability/fragility of the evp-code. For now, I do not care and just
233        update the verification experiment
234    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
235      - remove xx_genarr2d_numsmooth etc
236      - use xx_genarr2d_preproc etc instead
237      - carry out smooth_correl2D at initialization stage rather than during
238        time stepping.
239      - get smoothOpNb from xx_gentim2d_preproc
240    o global_oce_cs32 :
241      - add test of generic ecco capabilities.
242    o pkg/exf/exf_getsurfacefluxes.F :
243      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
244    o pkg/ctrl,ecco :
245      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
246        is defined.
247    o pkg/seaice: add diagnostics for Delta (deformation parameter)
248    o model/src:
249      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
250        diffusivity (background) is specified but ignored.
251    o verification:
252      - in testreport, convert hostname to lower case for default output dir name
253    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
254    o pkg/dic: add modifications from Hajoon:
255      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
256      - light attenuation: add self-shading effect by climatological Chlorophyll
257        (read from file).
258    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
259        compiles when SEAICE_ALLOW_DYNAMICS is undefined
260    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
261        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
262        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
263        approach where CPP_OPTIONS.h includes an omnipotent
264        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
265    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
266        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
267  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
268    to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included      to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
269    (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)      (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
270  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
271    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
272    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
273    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
274    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
275  o pkg/ctrl,ecco,exf :  o pkg/ctrl,ecco,exf :
276    - remove variables associated with NON-generic costs,    - remove variables associated with NON-generic costs,
277      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
278    - remove NON-generic NON-obcs controls,    - remove NON-generic NON-obcs controls,
279      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
280  o pkg/ctrl : added ctrl_local_params.h  o pkg/ctrl : added ctrl_local_params.h
281  o pkg/ecco : added ecco_local_params.h  o pkg/ecco : added ecco_local_params.h
282  o verification : added ECCO_CTRL_DEPRECATED to most as and oad  o verification : added ECCO_CTRL_DEPRECATED to most as and oad
283    experiments, which will progressively be removed once the      experiments, which will progressively be removed once the
284    experiments are revised to use only generic controls/costs.      experiments are revised to use only generic controls/costs.
285    
286  checkpoint65f (2014/10/13)  checkpoint65f (2014/10/13)
287  o pkg/ctrl, ecco, seaice : minor changes in headers  o pkg/ctrl, ecco, seaice : minor changes in headers
288  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
289    cost function and control capabilities added since checkpoint65c.      cost function and control capabilities added since checkpoint65c.
290  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
291  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
292    - ecco_toolbox.F (new) : basic operations that are often used,    - ecco_toolbox.F (new) : basic operations that are often used,
# Line 393  o pkg/seaice: more clean up Line 646  o pkg/seaice: more clean up
646      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
647      this experiment):      this experiment):
648      > size mitgcmuv_ad      > size mitgcmuv_ad
649      text    data        bss     dec        hex        text    data        bss     dec        hex
650      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
651      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
652      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
653      text    data        bss     dec        hex      text    data        bss     dec        hex

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