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revision 1.2107 by jmc, Wed Dec 17 17:58:39 2014 UTC revision 1.2173 by jmc, Sat Jul 18 22:15:07 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 pkg/offline:
8      - change where Offline-Fields are loaded, from load_fields_driver.F to
9        directly within FORWARD_STEP, just after updating iter number and time;
10      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
11        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
12       These changes allow:
13        a) to recover exactly on-line results using deltaToffline=deltaTClock,
14        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
15        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
16        time-step, both with GM & KPP files and with recomputing these fields;
17        b) no needs to switch on staggerTimeStep anymore;
18        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
19      - update output of experiments tutorial_cfc_offline (11 to 13 digits left)
20        and tutorial_dic_adjoffline (only 3 digits left).
21    o pkg/offline:
22      - change (rarely used) offset-iteration parameter to an offset time (in s):
23        can easily recover previous offset-iter effect by setting offset-time
24        (offlineTimeOffset) to offset-iter x deltaToffline;
25      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
26        in KPP as part of surface buoyancy forcing) in offline run.
27      - fix ptracers KPP non-local term in the case where KPP is re-computed.
28    o OpenAD
29      - Adding preliminary ggl90 test to OpenAD verification.
30        Config. with ggl90 currently diverges after 64 time steps
31        so will need more work to become more stable
32      - Adding preliminary kpp test to OpenAD verification.
33        required small tweakes in kpp_routines.F
34      - Merge and update from Krishna Narayanan's contrib area:
35        * Add one variable for preliminary OpenAD DIVA
36        * Add replacement time-stepping for OpenAD DIVA
37        * genmake2 flag -diva (but only for OpenAD; preliminary)
38        * required modifs for OAD_support
39        successful preliminary test for tutorial_global_oce_biogeo/
40    o pkg/seaice:
41      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
42      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
43        delta with a smooth function in s/r seaice_calc_viscosity
44        (no effect on EVP)
45      - rename local suffix "sqr" into "sq" for more consistent variable names
46    o pkg/seaice:
47        add new parameter SEAICE_deltaMin that is used ***only***
48        for regularizing Delta (and nothing else, like the parameter
49        which is also used for all sorts of things SEAICE_EPS).
50        Defaults to SEAICE_EPS for backward compatibility only.
51    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
52        the wrong key by inialising it before use -> fixes a recomputation
53        problem but does not fix the gradient
54    o pkg/layers:
55      - move resetting of flux arrays to outside the iLa loop
56        (this caused layers_diapycnal to not work with more than one layer coord.)
57      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
58    o pkg/layers:
59      - remove from common block 3D layers fields (used to diagnose transport
60        in tracer coords) and declare them as local arrays in layers_calc.F
61    o pkg/seaice:
62      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
63        in lab_sea forward experiment (changes results -> updated)
64      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
65    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
66       computations; for SEAICE_VECTORIZE_LSR
67      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
68        sweep to the outside,
69      - remove store directives and add "CADJ loop sequential" directives
70        in analogy to model/src/solve_tridiagonal.F
71      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
72        boundaries to yield more readable code. This has also the charming side
73        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
74        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
75        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
76        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
77        an additional option)
78       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
79       but the adjoint gradients (which are affected by this change) still explode.
80    o coupler (atm & ocn _compon_interf):
81      - avoid using Exch2 IO mapping if not suitable.
82    
83    checkpoint65m (2015/06/15)
84    o pkg/layers:
85      - clean-up old parameters setting (from Sep 2012):
86        + remove old parameters setting from common block (declared locally);
87        + stop if any old parameter is mixed with new parameters;
88        + check for valid or consistent parameter setting (e.g., layers_name)
89      - check that layers_bounds for Pot.Density are in the right range;
90        this is supposed to catch un-updated setting after recently shifting
91        potential density field "prho" by -1000 (now in "sigma" scale).
92    o pkg/layers:
93      - Added missing call to layers_fill for keeping track of tottend in
94        pkg/diagnostics/diagnostics_fill_state.F
95    o pkg/layers:
96      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
97        of diapycnal fluxes
98    o pkg/layers:
99      - reverted changes to interpolation to previous treatment; there
100        was never actually a problem
101    o pkg/layers:
102      - fix interpolation of layers tracers in the presence of partial cells
103      - add lots of new functionality to compute water mass transformation
104        (enabled by CPP flag LAYERS_THERMODYNAMICS)
105      - add new calls from main code (diags_oceanic_surf_flux.F,
106        thermodynamics.F, impldiff.F) and gad to save the necessary fields
107        for layers_thermodynamics calculations
108    o pkg/ptracers:
109      - add capability of stepping a passive tracer forward without advection
110        by setting PTRACERS_advScheme to 0.
111    o pkg/diagnostics:
112      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
113    o pkg/layers:
114      - shift potential density field "prho" by -1000 for density layer averaging so
115        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
116        Note that density bin boundaries (layers_bounds in data.layers) have
117        to be set accordingly (i.e., shifted, in sigma scale).
118    o pkg/layers:
119      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
120      - fix calculation of layer non-weighted velocity and layer probability
121      - add diagnostics for pot.density used for layer averaging
122    o pkg/seaice:
123      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
124        positiveness, modify a few comments and improve variable names,
125      - the changed computation of deltaC affects most seaice-related
126        experiments at the truncation level.
127        seaice_itd.thermo is affected by far the most, with
128        only 7 digits of agreement remaining; update experiments.
129    
130    checkpoint65l (2015/05/04)
131    o pkg/shelfice:
132      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
133        factor drKp1 to zero where it is negative (ie. do not use
134        SHELFICEBoundaryLayer if hFacC>1)
135      - the same for factor drLoc in shelfice_forcing.F
136    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
137        with modules in ptracers, when using testreport option "-small_f"
138    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
139      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
140    o verification/testreport
141      - add new option -small_f
142        with this option testreport first makes the target small_f (*.f files)
143        before running make (all). This is useful for explicit inlining when
144        all sources need to be full available.
145    o pkg/exf/exf_interp.F:
146        remove previous changes related to reverse (decreasing) input grids latitude
147    
148    checkpoint65k (2015/04/01)
149    o pkg/ecco:
150        fix missing cosphi initialization; use eccoiter in place of optimcycle;
151        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
152        instead of active read/write
153    o pkg/ctrl:
154        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
155        instead of active read/write.
156    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
157        return if .NOT.useAUTODIFF
158    o pkg/seaice: add CPP brackets (cost function related).
159    o model/src:
160        add useAUTODIFF run time switch.
161    o pkg/exf/exf_interp.F:
162        add code to allow input grids with latitude starting in the north (i.e. when
163        j=1 corresponds to northern edge of field); modify global_with_exf to test
164        this feature.
165    o verification/testreport:
166      - replace "grep -A3" with POSIX conformal sed command, because there are
167        implementations of grep that cannot do contextual searches
168      - replace "cat -n" by "nl" (two occurrences), because not all implementations
169        of "cat" have the option "-n"
170    o model/src:
171        add new file gsw_teos10.F that contains 3 functions, more or less a copy
172        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
173        convert from conservative to potential temperature. For now they are not
174        called anywhere.
175    o pkg/ggl90: make "useIDEMIX" useful
176      - re-organize code in s/r ggl90_calc a little to move computations that
177        are different for idemix into separate loops (changes verification
178        experiment idemix at truncation level, 12 digits remain -> updated)
179      - requires 2 new 2D fields KappaM, verticalShear
180      - make hFacI and recip_hFacI local 3D variables that are passed to
181        s/r ggl90_idemix
182      - fix and improve some comments
183    
184    checkpoint65j (2015/02/25)
185    o pkg/openad
186      - synchronize seawater.F with version in model/src: replace routine
187        body of sw_temp by calling sw_ptmp and fix/add a few comments.
188    o pkg/mnc:
189      - change default value of pickup_read/write_mnc params to FALSE
190        (since few features are missing in reading MNC pickup files).
191    o model/src:
192      - change default (background) vertical diffusivity for salt to be the
193        temperature (background) vertical diffusivity.
194      - change background vertical diffusivity in vertical mixing pkgs ggl90,
195        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
196        This makes ptracers default diffusivity (that uses salt diffKr) more
197        consistent with vertical mixing schemes.
198    o verification/testreport:
199      - fix typo in "-pcls" option ;
200      - put temp files in /tmp (instead of in local dir)
201      - add option "-ncad" to use genmake2 new option "-nocat4ad"
202      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
203    o pkg/ggl90 (idemix code):
204      - apply few fixes ; add some missing "_d 0" ; update output of exp.
205        global_ocean.90x40x15.idemix
206    o OpenAD
207      - enable active file I/O and begin removal of work-around code
208        for OpenAD for handling control variables (memory vs. active files)
209      - new CPP options file OPENAD_OPTIONS.h
210      - revert to genarr2d gradient check for hs94.1x64x5
211      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
212      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
213    o tools/genmake2:
214      - add option for an alternative Makefile (from Martin) where multiple
215        source files are sent to TAF (instead of all in one file).
216    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
217      - code provided by Carsten Eden as an extension of ggl90
218      - so far the code is turned on within ggl90 by setting a CPP-flag at
219        compile time; a runtime flag implementation is not yet complete
220      - tested in new verification experiment global_ocean.90x40x15.idemix
221    o verification:
222      - reduce length of the AD test run by half for experiments
223        global_ocean.cs32x15 (std + thsice) and isomip
224      - enable active file I/O for OpenAD, adjust verifications accordingly
225      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
226    o verification/testreport:
227      - fix two non-POSIX sed statements so that there are no error messages
228        on Mac OS X
229      - replace hostname -s with hostname | sed 's/\..*$//'
230    o model/src/seawater.F:
231      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
232        (following the matlab code), which would have avoided the bug caught
233        by Matt (see below) in the first place
234    o pkg/shelfice:
235      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
236        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
237      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
238        ice-shelf case (i.e., within surface level).
239      - add config summary in shelfice_check.F
240      - remove global variable recip_SHELFICElatentHeat and replace by a local
241        variable recip_latentHeat
242      - introduce diagnostics for friction velocity uStar (in case of
243        SHELFICEuseGammaFrict)
244      - change verification experiment isomip.htd:
245        + start from pickup (as input_ad at nIter0=8640)
246        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
247        + test SHELFICEuseGammaFrict = .TRUE.
248        + test SHELFICEadvDiffHeatFlux = .TRUE.
249    o model/src:
250      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
251        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
252        update output of experiments global_with_exf.yearly and isomip (all 6).
253    o pkg/shelfice:
254      - change setting of kTopC to also be zero where there is no ice-shelf.
255      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
256        ice-shelf is.
257      - first attempt to get RealFreshWaterFlux effects: for now, only without
258        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
259    o pkg/seaice: add the option to prescribe a fixed thickness PDF
260      for thermodynamic calculations
261      - because of divisions of the type 7/7 not exactly equal to 1, this change
262        affects results of some verification experiments by up to 4 digits:
263        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
264        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
265        adjoint: lab_sea, lab_sea.noseaicedyn
266        -> updated
267    
268    checkpoint65i (2015/01/23)
269    o model/src:
270      - change units of frictionHeating field from W to W/m^2
271      - fix bug in frictional heating from stratospheric drag in
272        S/R ATM_PHYS_TENDENCY_APPLY_V
273      - with synchronous time-stepping: move resetting to zero of frictionHeating
274        field from load_fields_driver.F to thermodynamics.F ;
275      - add diagnostics for frictional heating.
276    o model/src & gmredi K3D:
277      - add frictionHeating field to pickup-files (for synchronous time-stepping)
278      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
279      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
280        and name in pickup file).
281      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
282    o model/src:
283      - move (from ini_forcing.F) initialisation of all arrays in header file
284        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
285        (since Nov 2012) with option selectAddFluid=1.
286    o pkg/shelfice:
287      - change units (+ document) of newly added field "shelfIceMassDynTendency"
288      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
289    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
290    o pkg/seaice: two new runtime parameters:
291      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
292        long overdue
293      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
294        parameterization of tensil stress for fast ice (does not do anything yet)
295    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
296        for LSR: move checking overlaps out of JFNK-if-block
297    o pkg/atm_phys:
298      - move copy of grid and dynamical fields out of atm_phys_driver.F into
299        new S/R ATM_PHYS_DYN2PHYS.
300      - fix level height for Linear Free-Surf case (to be consistent with
301        fixed-in-time pressure levels).
302    o pkg/mom_common (bottomdrag):
303      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
304        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
305        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
306    o pkg/shelfice (u/v_drag):
307      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
308      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
309        (now similar to shelfice_u_drag.F)
310      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
311        from mom_vecinv.F (similar to mom_fluxform calls).
312    o pkg/mom_common (bottomdrag):
313      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
314      - add options for alternative discretisation of velocity norm in quadratic
315        bottom drag: averaging of grid-cell-center KE to U.point and V.point
316        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
317        improves when averaging only the other component (e.g. vVel for U bottom
318        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
319      - add options (bottomVisc_pCell) to account for partial-cell in bottom
320        friction (no-slip BC) thus getting the true distance from the bottom;
321        off by default since this also reduces model stability (explicit bottom
322        friction). Changes produce different machine truncation with linear-drag
323        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
324        front_relax (bvp & mxl, 10 & 11 digits).
325    o model/src & mom pkgs:
326      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
327        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
328      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
329        just copy level Nr value to level Nr+1.
330    o doc:
331      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
332    o pkg/streamice:
333      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
334        SHELFICE.h: move array shelficemass to init_varia, initialise
335        from array shelficemassinit, which is set in init_fixed and
336        has option to be set from file; introduce array
337        shelficeMassDynTend array, set thru file in init_fixed
338      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
339        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
340        pkg/streamice
341      - shelfice_thermodynamics.F: call shelfice_step_icemass if
342        SHELFICEMassStepping = .true.
343      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
344    
345  checkpoint65h (2014/12/17)  checkpoint65h (2014/12/17)
346  o verification/global_ocean.90x40x15, global_ocean_ebm:  o verification/global_ocean.90x40x15, global_ocean_ebm:
347    - update to generic controls.    - update to generic controls.

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